You're right, sex toys don't cum. However, as the post above me pointed out, some sex toys need lube. And even if they don't, they still need to be cleaned thoroughly after each usage. A condom is a good way of keeping toys clean--I even know of a few adult websites that recommend this. Also, it's entirely possible she was using something that was not a sex toy for sexual purposes, and wanted to keep things clean down there.
I wouldn't jump to the conclusion that she's cheating just because of the condom. But if you have other reasons to suspect foul play, then definitely try and find out what's going on.