Maybe you could make a dinstinction between 00:06:729 (1,2,3) - and 00:08:119 (1,2,3) - as they are both stacked but one is 1/4 rhythms and the other is a triple which could be missleading.
You could space one of these two a little bit so they are not similar and this way make the difference in rhythms more clear
00:59:561 (3,1,2) - These objects are quite hard to read as they could be easily mistaken as a 1/2 rhythm stacked, players could tap it like that and might miss one of the notes or get 100/50 points, then for 01:00:179 (1) - that is now part of the 1/2 rhythm is spaced oud, could be read in a different rhythm too. This whole pattern can cause combo breaks.
I think it's best if you move circles around so it's a bit more clear what the rhythm truly is to avoid players reading this wrong.
02:34:103 (1,2,3) - This pattern is a bit confusing considering you already introduced patterns like this but as 1/8 rhythms (i.e see: 00:10:436 (3,4,1) - and they both look the same.
It would be better to have a difference between both patterns since there is a difference in rhythm, perhaps doing control + G on 02:34:566 (3) - could be a way to fix this.
If you agree with this, apply the change in other instances of this kiai where this happens.