When I worked at arXiv one of my coworkers was a fresh astrophysics PhD who was cynical about the state of the field. He thought that we didn't know what the hell was going on with accretion disks but that a few powerful people in the field created the impression that we did and that there was no dissent because it was so difficult to get established in the field.

When I first saw the ΛCDM model my first impression was that I'd didn't believe it, it seemed bad enough to have dark matter that we didn't understand (though WIMPs and axions are plausible) but adding equally mysterious and physically unmotivated dark energy made it seem just an exercise in curve fitting.

There have been a longstanding problem that the history of the universe and cosmological distance scale haven't made sense.

https://medium.com/starts-with-a-bang/the-hubble-tension-sti...

When I was getting my PhD in condensed matter physics I was going to the department colloquium all the time and seeing astrophysics talks about how some people thought the hubble constant was 40 km/s/Mpc and others thought it was 80 km/s/Mpc. With timescape cosmology maybe they were both right.

Another longstanding problem in astronomy is that since the 1970s it's been clear we have no idea of how supermassive black holes could have formed in the time we think the universe has existed. With the JWST there are a flood of results that show the first 500 million years of the universe probably lasted a lot more than 500 million years

https://iopscience.iop.org/article/10.3847/2041-8213/ac9b22