Although they are technically illegal to have it is difficult for them to enforce as the owner just claims the cat isnt theirs and will dump the kitty outside.
Many bodegas dont bother to fix the cat or vet them and as they often go outside they are prone to illnesses like FLK and FIV.
I would try to make a point to talk to the owner about the kitty to get a sense if they cared for it or not. I have TNR'ed several bodega cats with varying degrees of success as some did not provide any post-op care for the cats and they became ill post surgery but were left to die as they didnt bother to take to a vet so I had to rescue them myself and vet them myself while they just went out and got a new kitten.
I would politey be nosy to see if the cat is fed, watered and has a litterbox, ask if it is fixed and vaccinated - sometimes they let them get pregnant and sell the kittens.
If you think the cat is ill you can call the ASPCA on them but again they will just claim the cat isn't theirs and dump it on the street or take it to the ACC to be killed. It is hard to prove the cat is theirs if they claim otherwise and hard to get the A to take it seriously to investigate as laws are so weak. Take pics if you see an ill kitty with time/date stamps on them discretely for your own safety.
Most bodega owners I have met are open to their cats being fixed and vaccinated through TNR as there is little to no cost to them. I think it's like $5-7 for the FVRCP vaccine and another $10 for flea medicine and if it's a boy a few more bucks for dust free litter to use post surgery. Some have even repaid me for my efforts but I don't bother to ask as fewer kittens being born for me to rescue is payment enough.