Is there a way to filter for token. When I put a filter with only type token a lot of them are missing and it does not look like it is coming from the type because I have some that are there and some not.

Would you mind giving some more info, like examples of the ones that are missing?

I'm not seeing any issues in my own inventory. When I filter to tokens and emblems (either using Type of Type Line), it gives me 247 unique results, which is correct (I actually have 807 total tokens, but Deckbox doesn't show that number in the filtered list, unfortunately). My tokens span from recent sets (latest is RIX) all the way back to 10 Ed. / Lorwyn, and include tokens from regular standard sets, masters sets, commander decks, duel decks, and even promos (like the Magic Player Rewards). The filters even catch "tokens" like Checklists and Poison that aren't part of the official token numbering.

Are all your missing tokens part of the same set(s) (especially sets that are more recent than Rivals, which I can't check)? If so, I'm betting those specific editions were just added to the database incorrectly.