If you have line numbers, I'm quite sure you are not using Vim's yank/put operations (these will never copy the linenumbers, foldcolumn, icons etc) because in terms of the edit buffer, they don't exist.
My guess is you are working in a terminal emulator and using the mouse to copy stuff to the clipboard, which possibly selects the 'extraneous' room of the screen (including virtual spaces at the end, line numbers, fold markers etc)
You might have luck setting
:se mouse+=a
in order to get the behaviour of the mouse like you expect it. Otherwise, do the selection with V<movement>...
y (y
for yank
, which corresponds to 'copy')
Then on the destination use p (put at cursor), or P (put before cursor)
Let me know if that helped or you need more info
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…