I don't think those are guts that you are seeing. More like yolk and or their waste. I'm not an expert, but when I hatched out my ducklings before, that is what I read and saw.
What color were these guts? I don't see how it could be the gut since their inside develops first, and development is internally. Guts don't develop first and then somehow move back into the duck's body.
Your temperature is way too low. 89.9 is too low still. Maybe you were able to hatch out duck eggs before, but for correct incubating times, it is suppose to be around 100, give or take.
I don't think its the mother duck. But I think you are breaking these eggs upon prematurely. If you candle them, you can see their size and get an idea. No need to break open the egg to see them.