We harvested a lot of lemons from my FIL's big Ponderosa lemon tree.

The normal lemons are huge and bumpy and we love them as they are super juicy. However this year I noticed that while the majority are still showing the normal huge and bumpy, others are smooth and orangey. And when we tasted one of the fruits, still super juicy with slight tartness but definitely not as sour as the big bumpy ones and with hint of sweetness. My FIL's neighbor has a huge orange tree also loaded with fruits. Is it possible that the lemon blooms got crossed with oranges pollens. And if I plant the seeds, will these produce new varieties?

Top one are the big and bumpy, the smaller:

Carefully dissect a seed and check for multiple embryos - they will look like thin wavy layers tightly stacked on top of one another inside the seed coat. If there are multiple layers (polyembryonic) the seed will be just like whatever fruit it came out of. If its just a single embryo seed (monoembryonic) it will be a hybrid of the mother tree and whatever pollinated it.

But... changes don't show up in the fruit, they show up in the seedlings grown from the seeds inside the fruit. Can you remember if all the orange-like fruits were on just a few branches in the tree or scattered on the branches in amongst the ponderosa lemons? Hopefully you will say the orange-like fruit was all on different branches because if you don't, we may have to re-write all the books on citrus genetics. I'm going to assume the orange-type fruits really are oranges and that your FIL's tree is grafted onto a sweet orange.

I can't recall but next time I go I will take a photo. These are probably the juiciest lemons I've seen. 3 lemons can fill in a cup. I wasn't paying attention until I got home and noticed the difference in both the size, the skin texture and the taste.

They're sometimes hard to spot, especially if the tree is more of a tree sized bush, but look for stems coming off the main trunk somewhere near ground level. Hopefully there are some slight differences: less/more thorns, different shaped leaves...

Here are some photos, before we picked some:

The lumpy fruit seem to be grouped together and the smooth ones seem to also occur in like bunches which might suggest the two types are on different branches.