Belthasar Clairvoyance Inconsistency
In 2300 A.D., the party can visit Belthasar after first arriving. There, he is shown to be working on the Poyozo Dolls, and mentions that the party will eventually have to climb Death Peak:
OLD MAN: NO! You MUST NOT climb Death Peak! Wouldn't make it very far, anyway! It has to be the right time... ...and...THEY...have to show you the way!
How did Belthasar know Crono was going to die, let alone that he'd perish in the Ocean Palace? How did he know that Gaspar would give the party a Time Egg which would be taken to the top of Death Peak? For that matter, how does Janus know Crono is doing to die beforehand? This ability implies that the future is known can be read, which is erroneous; everything about the Chrono series suggests that time is malleable and the future is shaped according to the will of the present. Since there is no predestination, how do they know that Crono will die?
Let's assume that Janus could feel the Black Wind. Masato Kato authored all of Zeal, including Janus's prophecy, but it may have just been dramatic foreshadowing. If Janus knew Crono would die, why didn't he know several others would too? Why didn't that apparent clarity tell him (let alone other people who can feel the Black Wind and are older, like Schala) that the Ocean Palace was going to explode? But not even considering Janus, Belthasar had to have the foresight to know Crono would die several days, or even weeks beforehand. The Retranslation tells us that he prepared the Epoch as a way to return home, but had to abandon his work in the end and leave it to the party. Pegging an ability to feel the Black Wind leaves too much unaccounted for.
Time Egg Plan Switch
This theory assumes that the Entity is what caused the eclipse and helped the party go back to the Ocean Palace. Gaspar communicated to Belthasar a plan to use the Time Egg on top of Death Peak to try and defeat Lavos; perhaps the Time Egg was even designed to go to that instant in the Ocean Palace so that Lavos could be defeated there and prevent Zeal from falling. Gaspar was aware of the Entity's plan to use adventurers at this point, but did not use this plan as the party were going to arrive in Zeal anyway, it seemed. Belthasar still assumed it would take place, and made plans to allow access to Death Peak. All that changed when Crono died at the Ocean Palace and the party could not defeat Lavos there, suggesting to Gaspar that they weren't ready (and thus needed the sidequests and more time). Gaspar still had the Time Egg on hand, and decided to give it to the party and make use of the original plan so that Crono, a very powerful warrior who could help defeat Lavos, could be revived and the mission completed later. So he corresponded with Belthasar, or perhaps Belthasar knew some other way (this is iffy).
Issues include A) this means Gaspar corresponded with Belthasar. It is not proven that the Gurus had any real communication. There is still a slight basis for this since Belthasar in the Nu does talk of the entire quest against Lavos; B) this assumes that the Nu is sentient; that it doesn't just have prerecorded messages, but could think enough to know that the original plan was scrapped and the party intended to revive Crono, C) We're assuming Gaspar had the double intention of saving Zeal along with defeating Lavos at the Ocean Palace, and D) the entire game is still geared towards the original narrative that Belthasar knew EXACTLY what he was doing all along and that Crono would die. No way.
From: Plot Inconsistencies