Some specific Construct limitations off the top of my head, there are probably more.
No running when window is not focused.
No FPS rate limiting controls.
Certain things will run more efficiently/faster with pure JS, vs behaviors. The normal user is unlikely to run into this as a problem, until really pushing the limits of what a device can do. But then you can just use JS, so it's not really a limitation.
Various issues with using HTML form elements, which float over the canvas.
Jankiness with high cpu use (on certain platforms?), even if FPS is high. (This one is being actively looked into AFAIK and should be fixed, more of a bug than a limitation)
I mean to be honest making a mining node that spawns a mineral and throws it in the air and then collides on floor
This doesn't have anything to do with an engine limitation.