I ran into similar issues listed in this thread. I am (somewhat) happy to report they were user errors. :-P
1. I was a bit baffled at the client build listed as 15050, when I knew my client was 15595. The client was fine. The error was that I compiled the tools from the master branch, which is pre-CATA (i.e. 3.3.5.a 12340). Obviously, that will not work. Once I switched to 4.3.4 branch and recompiled the tools, things worked well. I think it would be good to have the tools list the WoW client build they are meant for, like printing "Map & DBC Extractor for 3.3.5a clients".
2. When running the vmaps4assembler, I got this message: ("Could not read dir_bin file!"). I looked at the source, which gave me a hint this had to do with the sourse directory (server/collision/Maps/TileAssembler.cpp: std::string fname = iSrcDir + "/dir_bin";), so I looked in "Buildings". I found it was empty, due again to the wrong tools version, which lead to vmaps4extractor not working. If I recall correctly, even though the output indicated errors, the last message seemed to indicate that there were no errors. Anyways, once I used the right level of the vmaps4extractor, Buildings was properly populated, which then lead to a successful vmaps4assembler run. I think it would also be good to have the "Could not read dir_bin file!" message be more descriptive, like "Could not read expected input in source directory <<DIR_NAME>>, please ensure you are not a noob and have the right files there!".
Overall, these issues can be avoided if the users carefully understand and follows the instructions, but a bit more user feedback during the runtime would help identify user errors more quickly.