This is a tough call.
A year ago, I had a queen who left perfectly healthy kittens on the floor outside her bathtub nest. I'd put the kitten back and later find different kitteb alone and shivering on the floor. Sadly, I didn't realize until she placed the fourth kitten out there that she wasn't feeding him properly. Poor little thing didn't make it. But the others did. Remember, each situation is different and each queen is different.
I always put them back, unless I see something's wrong or she pushes the same kitten aside several times. I also watch very closely. If you suspect there's a problem, take the kitten to the vet.
If you find a litter of kittens in a field or under a bush, check them out before carting them off. I go into a lot more details in "Kittens For Dummies" but if they're clean and well-fed, mom's probably watching from a distance, unless you find her body. Dirty, crying kittens need your help.
Also, I see you are involved in feral rescue. If it's a feral situation, I'd get mom fixed as soon as the kittens are weaned. Sometimes it's hard as heck to catch her. As cruel as it sounds, I stop feeding her and only leave food in the trap until after she's had her mind and body altering encounter with the neuter vet.