This is a weird Hammer error. It can be from a few different things, but it usually happens when you have a fatal problem with the map (invalid brush, etc), which means required files cannot be created. The compile script continues, however, and when it reaches the point where it needs those files, they aren't there, so you get this error.
Check your compile log for errors. If you're using the default compile tools, though, (the ones that came with Hammer), then they're not going to be very informative. If that's the case, then download the ZHLT compile tools from
here. You set them up to work with Hammer, by pointing it to those executables instead of the given qcsg.exe, qbsp2.exe, etc. If there's many things in the compile log you don't understand, then post it here (make an external link to a .txt file if it's very long) and we can take a look at it. You should also have Hammer check the map for problems. Go to Map->Check for Problems, or hit Alt+P. This isn't guaranteed to find all problems, and it will sometimes report problems that aren't big ones, but it can help you track down an issue sometimes.
And yes, you could also try the
ZHLT Compile GUI if you wish. I use an old version of it (v8 I believe) to compile my ESF maps.