When using the clone command, it clones the stuff to a wrong position.
To reproduce it, simply clone whatever you want, then clone it to a space by using ~s. It is recommended to reproduce this bug by typing it instead of using command blocks as I only use typing for the test, but you can use command blocks to see if it can reproduce the bug.

In my observation, this bug occurs due to a command bug occurs, causing incorrect placement of beginning/ending/destination coordinates.