The jars shall be removed from the canner. Few reasons (there might be more). One - leaving the jars in the hot water keeps the content cooking and some things like veggies or fruits become mushy when "overcooked". Not like there is any crunch after pressure cooking, but the consistency is not very appealing. Two - jars need to be cooled down in slower & controlled pace. That`s why you`ll see the jars wrapped in an old blanket overnight. Three - jars do break from time to time, and if it happens inside the canner, it gets diffucult to remove the shards and the rest out and not to get injured not to mention the cleaning the whole thing.
If the vacuum does not seal the lids completely "suck the lids in" without popping back, I would not trust the content for longer therm storage. If it happens put the jars in the fridge and consume within week or so.
How to get a good seal? Lids can be the culprit - use different brand or kind. It doesn`t really matter whether one or two piece. Use something that works. Clean your jars thorougly before the canning. Some people literally boil empty jars without lids in the water for a few minutes. When pouring the content in the jar, use a funnel - really go get one - they are cheap and keep the top of the jar clean. Smallest amount of anything in there will compromise the seal.
Good luck canning!