Well in my opinion just having too much stuff can cause lag, optimization of missions involving near BoE situations (only assuming that's what this Mystery Project will have based upon Shadow Genesis) can be very difficult, especially with high poly models and such.
As for mistakes, well, at least in my experience poor organization of files can create mistakes, just look at my Dusk Wars mod, up until what I'm working on now I had 0 organization skills and never prepared properly and I'm paying the price for it. However this was causing show stopping bugs not slowing performance, I'm not quite sure what can slow a game's performance beyond what Blue Planet has learned* and what I said above.
I'm sure someone with more modding experience then myself could shed some light

*Poorly optimized Karuna