It has been said that a good model railroader is not someone who doesn't make mistakes, but someone who can correct his mistakes.  This simply means that noone is perfect, and mistakes will be made.  It's a part of learning.  This page lists out some of the major foulups that I have made while building this layout, in no particular order, which are things that you can learn to avoid.  Another thing to take away from this is: Don't be afraid to make mistakes.
 
Turnout Machine Access -  One of the things that I failed to plan for when building my layout was access to the turnout machines, and I should have known better.  Most of them happened to be accessible to begin with (as accessible as they can be, anyway), whether from the side or from below, but two of them were located away from the edges, in higher elevations.  I had to cut access holes in the 1/2" plywood framing for access to the machine for the turnout at the end of the trestle, and the machines for the two turnouts of the Blue Creek spur.
 
Turnout Ballasting - The reason why I was forced to create an access hole for the turnouts was that I made a mistake when I ballasted the Blue Creek spur the first time (I have since removed that ballast, and re-ballasted with a different color).  I had spread the ballast out into position, then I wetted the ballast down, and applied diluted white glue (the method I use everywhere else).  The problem is that the diluted white glue leaked down the hole that was cut for the actuating rod from the turnout machine.  This actuating rod not only operates the turnout, but also operates a switch that is mounted on the bottom of the turnout machine.  This switch changes the polarity of the frog wires.  When the diluted glue syphoned down the actuating rod, it got into the polarity switch, locked it into place, and ruined it.  So now, I somehow have to get the switch off of the turnout machine, and replace it.
 
Update: Recently, the layout was being moved, so I took the opportunity to set the layout on its side (for better access and lighting), and I removed the ruined switch from the turnout machine with a Dremel tool and hobby knife.  As I surmised, there was dried white glue all over it, and the bottom of the turnout machine.  I cut the wires off of the old switch, soldered them onto the new switch, and mounted the new switch onto the turnout machine.  Once again, I can run engines into the Blue Creek spurs!
 
In the meantime, I avoided the same problem on the other switches by ballasting as normal up to the switch.  Then I would put some ballast in a paper bowl, wetted it down, and soaked it in diluted glue, creating a sort of ballast paste.  I then applied the "ballast paste" with a toothpick to the turnouts from the frog to a few ties beyond the points.  This took some time, but with all of the narrow spaces and moving parts around the turnout, it actually was no more work than my normal methods.  It actually resulted in a neater job too.  
 
Using Sandpaper On Track - I brush-painted my track, and merely cleaned the paint off with medium grit sandpaper, and I would occasionally use sandpaper to clean the track.  After some time, I noticed that the painted track became dirtier much more quickly than the unpainted track in the tunnels.  At first I wondered if it had something to do with the paint that I used, but I eventually realized that using sandpaper on track will cause the track to gather much more dirt.  Now that I clean the track with rubbing alcohol on a rag, and have run many more trains over the tracks, it doesn't seem to get dirty as quickly.  Now I understand why some people go to great lengths of covering the tops of their rails with oils or the like before painting track, so that they do not need to use sandpaper to clean the paint off.  I've also polished the top of some of the rails with very fine grit sandpaper, to see if it will rectify that problem.
 
Tunnel Clearance - When planning the layout, I realized that any decrease in the amount of elevation the track has to climb would be a benefit, and in such a small layout, every millimeter counts.  So, I first made some measurements on my highest possible car (which turns out to be a 50' flatcar with a trailer on it).  I was then able to decrease my clearance from 2 inches to 1 5/8 inches.  Then, there are two locations where a tunnel goes under another track (one place is under the diamond crossing, and the other is where the passing siding/mainline crosses over the lower loop).  I realized that I could cut a path though the 1/2"  homasote subroadbed at those locations, the track could span the gap by itself, I just needed something thin to support ballast and other scenery.  The picture below shows a mockup for testing clearance in the tunnel near the entrance to the staging tracks.
In the picture, I temporarily placed the black foam roadbed (from Woodland Scenics) and some spare code 80 sectional track where the tunnel track would be located for the lower level.  I then placed a car box where the upper track would be located, and tested clearance with the 50' flat car with a trailer load.  The clearance worked well, and with this approach, I was able to decrease the elevation between tracks from 2 1/2" to a total of 1 5/8", which made a huge difference in the grades.
 
Once I checked for clearances in both locations, I added some thin sheet balsa wood to cover the gaps.  I then cut down the black foam roadbed in these areas to make up for the less than 1/16" "bump" caused by the balsa wood.  Like the homasote, the balsa wood would get damp occasionally when items were added and glued to the layout.  Unfortunately, the balsa wood under the diamond crossing warped into a sag one time, and did not return to it's original shape when it dried.  This warping is severe enough that my piggyback car would then get wedged in the tunnel.  I now have yet to figure out how to get to the underside of the balsa wood to correct the situation.  In the meantime, during operations, there is a "height restriction" in that tunnel, and the piggyback car cannot go through there.  Of course, the piggyback cars work fine through the more accessible location near the entry to the staging tracks.
 
I could have avoided this completely by using sheet brass instead of the balsa wood, like I was considering at the time.
 
Ballast Color - I had some Woodland Scenics light gray ballast left over from the mid-eighties, and so I started using it on two sections of mainline, and in the Blue Creek spurs.  Once I used that ballast up, I got some more from my local hobby shop.  It turns out that in the almost twenty years, the color has changed slightly.  Adding the new stuff next to the old stuff looked very patchy, and I did not like it one bit.  Also, the light colored ballast in the spurs made those tracks stand out a bit more than I wanted, so I wanted to change that to a black ballast, that visually makes the rails seem thinner.  So, I ended up removing every inch of that ballast (some six feet worth) by basically chiselling away at it with a hobby knife.  I wasn't able to get every little grain off, but it was close enough to the new ballast that the few remaining grains blended in, and I simply reballasted the mainlines with the new ballast.  For the spurs, I re-painted the track, which covered up the few remaining grains of ballast.  I could have planned the color of the ballast in the spurs better, but the difference in ballast shade wasn't something that I could have predicted.  Things like that will happen, even if you don't cause those mistakes.