When something can be predicted in advance to an exact moment - for example an eclipse which Chazal say it is a bad Omen (Sukkah 29A), does that mean that Chazal were unable to calculate this? Or perhaps even though they were able to calculate an eclipse it is a bad Omen?
It doesn't make sense to say that something predictable and cyclical is a bad omen. It's like saying the seasons, which occur every year, are a bad omen. The case of eclipses are just further apart.
The achronim assume Chazal knew what they were talking about when they said מאורות לוקין, and assume that they knew how to predict eclipses (I'm not sure if that's the historical consensus), so they want to give a different explanation of that gemarra.
One is the Aruch LeNer Sukkah 29a. He felt the term "בזמן", at the time of, was extra. They should have just said when חמה לקה. Rather it's referring to the time period when the eclipses occur. Yes the phenomenon is predictable, but Chazal knew this specific time was a time of דין, judgement.
The other is the Yearos Devash, Chelek Beis, Drush 12. It's referring to something that sounds like sun spots. Some blotch on the sun blocking its light (although I'm not sure how to this would be true for the moon).
You could also say it's referring to something that doesn't occur anymore, but I don't know if any source suggests that.
A short synopsis from here:
Now, you, I and the Jewish sages of old all have known for a very long time that eclipses are natural events that can be predicted thousands of years in advance. Thus we can be quite certain that their statement does not mean that eclipses are results of ill behavior. Rather, an additional result of the celestial positioning that causes an eclipse is that certain people are especially prone to sin and punishment. This is not unlike the Talmudic teaching that people born under certain Zodiac signs are likely to follow certain paths. These factors do not take away of free will, but they do give us a propensity that we can and must overcome.
This is why the Talmud (Sukkah 29A) concludes "But when Israel fulfill the will of the Omnipresent, they need have no fear of all these [omens]" (translation from here)