They look fine to me. The spots are thin areas in the shell.

Keep in mind that reptile eggs are adapted to allow some bacterial growth on the outside of the shell. Crocodilian eggs actually rely on this to thin the shells so the hatchlings can break through. So, you may see some discoloration over time, particularly where those thin spots are.

As long as the eggs don't dent in completely, discolor all over, get slimy, and get rubbery, they're fine.

Look at these ugly things:


The ugly eggs have looked that way since 20 days into incubation. Now, they're at day 50, and I cut one to take a peek. No problem, healthy fetus inside. They should be out on schedule (usually 56 days, not 60, for me).