I'm not sure, but it looks like SW 2015 handles assemblies in a slightly different way, I had the same issue I tracked it down to having a copied toolbox part
in the assembly, so I had two files in different sub assemblies within a top level assembly called the same thing one with all the need configuration one with out. If I opened the individual sub assemblies all was ok, because the need file was opened.
This did not happen in 2014, this is probably a good thing as it highlights potential problems, but if that's the case some sort of warning would be nice as come across as just a missing file.
Well the problem is that even the small sub assembly's are missing parts when i open them. So i can't open a assembly normally without having to individually click and pick every part. So thinking about downgrading to SW'14 again until this problem has been solved by SW or if somebody has a fix for this problem.
So if somebody has a fix or has the same problems please let my know!