Anyone else here find that using the tooling API to pull metadata down from Salesforce will occasionally just skip a file or two (or five)?

I swear that every time I clean my project in my IDE (Atom, using MavensMate) or through MavensMate directly, it ends up missing some random files (and different ones every time). This last time, it was a trigger (it had the .meta-xml file, just not the actual .trigger file). I also think I remember this happening when I was still using Eclipse + Force.comIDE