Firstly, are you using the latest version of TotalSpaces2?
But this may not fix it - I believe (from this earlier discussion Microsoft Word / Exce / PowerPointl (2011) not changing spaces properly ) that those microsoft programs also do this when using just Mission Control.
If that’s the case, then I’m not hopeful I can easily fix the issue - when the system demands a space change, TotalSpaces2 can’t usually ignore it, unless I can figure out a universal rule for that circumstance.
But anyway please let me know if it happens just with Mission Control and we can take it from there.