The only guess I have for this is my level…
When I discovered my first Beedrill, it was CP 172, and it broke out of 4-5 pokeballs before capture. After registering in Pokedex, then added to my collection, it was CP 56, a loss of 116 CP points.
This is the only time I've noticed a CP # different to what it was when entered into my collection.
Best Answer
The CP (and IVs for that matter) do not change from the time you encounter a Pokemon to the time that you capture it.
I have not personally encountered this, but I suspect it is a bug.