I'm not an expert IME I would say that it's a pollination problem

So does that mean the one with round end are pollinated properly?

I don't think there are various kinds of pollination, good, bad etc.
My guess (just guess) is that the seed had been crossed. So it has traces of two kinds of squash in it. If it is HYBRID, it has not been fully established. I can see that the two squashes on the vine even have different shapes and the one you've picked has yet another shape.

But the bottom line is getting fruit that taste good. I would not care what shape or color it is.

The one with the round end is good.

The other may be incompletely pollinated, but whatever the reason it was starting to rot on the yellow end.