1. Why do Gates sometimes lead to their other end and sometimes directly to the End of Time?
At first, the gates you enter lead to their other end. Then, they lead to the End of Time. Its possible that Gaspar has done something to make the End of Time as a cross-roads for Gates, with him being the Guru of Life.
2. Who really caused the Ocean Palace Incident and other anomalistic distortions?
Ocean Palace Disaster: I believe it was simply a side effect of the Mamon Machine overreacting due to the Red Knife being stuck into it. It caused Lavos' powers to create gates, which gated the Guru's and Janus. The Entity may have had a hand in deciding where those gates lead, due to the gates wouldn't have been a conscious decision by Lavos to make them (they would have been made by the Mamon Machine, techincally).
Marle's Pendant Reacting with the Telepod: The Entity created a gate at Leene Square, to try and prevent its death by use of Crono. The Telepod energizes the Pendant just enough to produce some sort of magical reaction, opening the gate.
Magus' Summoning, and the gating: Lavos was awoke, and used his power to smit Magus. Originally, Magus was able to complete his summoning properly, without disurbance. But when Crono and Frog assualted him, the summoning cerimony was thrown into chaos, and resulted in a situtation similar to the Ocean Palace Disaster, though a bit different. The Entity may have taken advantage of this situation as well.
Melchior and Janus' disappearance in 12000bc: I'll go with the Time Bastard here.
3. How does Lucca get the original version of Doan from ruined 2300 A.D. after defeating Lavos?
Plot. Hole.