The brooder is a heated chick pad in my garage which is 72 degrees and I have been carrying the sick chicks around in a sweatshirt with a hand warmer and making sure it doesn't get too hot in there. I hatched 16 chicks total and the 2 that hatched a day late are the ones with a problem everyone else is active. I used a hovabator Genesis with fan and turner with a hygrometer inside to monitor. Temps and humidity looked correct through incubation but may have been altered too much at the end when I opened it to take out chicks that hatched early.
Did you calibrate your thermometers, and how? If you did not calibrate them, then you can't trust what they are telling you. The issues you are seeing would not have been caused by opening the bator at end of hatch.