Yes it means appetizers, things you order and eat before a main course.

appetizers? I'm not sure, though.

The joke is that Michael Scott does not know what he is saying, and his confusion is both frustrating and charming. "Eating apps" or 'appetizers' makes grammatical sense, but means nothing in the context of goofing off at work. So he is likely confusing the kind of 'apps' that you eat at some restaurants and 'apps' that people use on their phones when they should be busy with work.