Well. It all started with the fact that one of my colleagues noticed a similar bug. A few hours later I was asked to create one large region on my server with based on PMMP. And it did not work out. The fact is that my RegionGuard plugin on is arranged so that the player needs to click on point 1 and 2. I clicked on point one, and region was created.

I made some changes on this line:

https://github.com/pmmp/PocketMine-MP/blob/master/src/pocketmine/Player.php#L2363

If you click on the block with your hand or item, the server will count it not for 1 click, but for 2 or more. However, I was informed that if I use block to click, everything comes back to normal