I have checked out the glitches you have noticed, and I have fixed most of them except for the following ones:
TM Double-ups:
[*]I forget where but you get TM40 Aerial Ace pretty early in the game long before beating the Flying Gym which rewards it again.
[*]You get TM02 Dragon Claw from Steven and then the same TM for beating the Dragon Gym pretty shortly after.
Seemingly Minor:
Talking to Riley in Vrai Cave again after beating him will lead him to ask you how all 3 Sinnoh starters are doing instead of just the one you chose.
These are all related to the content the creator added, so I'm not going to touch these, the rest should all be fixed. However, I'm still not sure how all those events reset because I have tested the whole game for many times and that didn't happen, I assume that is somehow related to the bicycle glitch, but I'm not sure, for now, I think the best way to completely fix it is to restart and try not to use the bicycle again(Unless you want to help me to test out if that is really fixed and make a copy of your save file before that).
The patch was updated to fix the following glitches:
Removed the Pokemon Center 2F for good to prevent the game from freezing.
Removed three TMs which can be obtained twice.
Fixed the glitchy bicycle(But I'm not sure if it is completely fixed)
Fixed some Pokemon's base stats, leveling rate and pokedex entry.
The move tutors of Mekong City.(But the fix won't work if you have already talked to them)
...And so on.
The old download link still works:
https://www.mediafire.com/file/suvlq8kk4gsrerv/Sienna+Complete+Version.ips/file