Thermometers can b so frustrating! No..it should not rest on the egg or touch anything. The sensor should just dangle. It's always best to use a couple of thermometers. I keep 2 in my bator that show temp & humidity. I generally incubate @99.7 w humidity @ 40% then raise humidity to 70% when they r due to hatch. Sounds like u have a humidity issue. If the eggs are to dry inside they can't pip through..or rotate in the egg to hatch.
 
A chick can take 24 hrs to pip from internal pip..and 24 hrs to hatch from external pip. Once they pip externally...thats when it become really dangerous to the chicks to open the bator. A chick can dry out and be unable to hatch just from opening the bator one time. If I must go n2 my bator at that point, I put a cup of hot water inside to bring humidity up quickly.
 
Humidity during hatch is crucial. the chick cN miterally b shrink Wrapped if it was to low.If u suspect ur humidity has been to low..u can try putting a small cup of hot water inside and bring it up to 80%.
 

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