All of these (except maybe 2, I haven't done Grand Duels in a long time) have been around for a long time...
1 - Turn order bug has been stated by many players, but it isn't limited to Tortures only - any indirect damage (including the reflected attacks and damage by Mirrors) will trigger it.
2 - You cannot change the skills of monsters in Grand Duels. Also, this one might be intentional but nevertheless is awful: there are no warm-ups on Grand Duels and it heavily diminishes the experience (for me, at least).
3 - The generation of Maze Coins by breeding and hatching is still very wacky and unstable, but I have noticed a trend that happens sometimes; the game awards you the same number of Maze Coins as the last breeding you did gives you. For example, if I bred 2 monsters and that awarded me 47 Maze Coins, the next egg I hatch, whether I wait 4 hours or 40 hours, will give me 47 Maze Coins. Likewise, if my breeding times on my Tree and Cave mismatched and I bred some monster while my Thunder Eagles were breeding and got 6 Maze Coins out of it... well I'm going to get 6 Maze Coins out of the next monster I hatch.
I know breeding Pandakens and selling that egg will bring us up to speed, but this demands 2 open Hatchery slots at all times, and since Mazes and breeding events tend to happen simultaneously, a lot of Coins get lost in between. Also, since by breeding Pandakens we make that our last breeding combo that naturally gives us 0 Coins, the next egg we hatch is also going to give us 0 Coins, making for a very clunky experience.