I've been able to copy/paste the whole image into another document, without any problems. At least, not that I can see.
Oh wait, when you say "hole pattern", do you mean copy/paste just the holes? I thought "hole" was a typo and you really meant "whole". But maybe you really mean you only want to copy/paste the circles?
Hhmm, no, I didn't have any problem with that either. It might be a case of - just try again tomorrow, and it will work ok. I don't know why, but that does seem to happen sometimes.
I do see one potential problem. I don't know if it would cause the problem you're having, but maybe. But it could definitely cause other problems.
A lot of the circles ("holes") are clones. But a lot of those are Clone of: Clone of: Clone of: Clone of:..... So instead of clicking the clone button (or key shortcut) repeatedly, you need to reselect the original circle each time, and make a clone directly from the original every time, instead of from another clone. (Or if you need a large number of clones, you can use Edit menu > Clones > Tiled Clones, to create a lot all at once.)
Fortunately, you can fix all the nested clones at once. Just do Ctrl A (select all) and click the button to break the clone's link to its parent (or the key shortcut). That will turn them all into paths.
If I select only the circles which are paths, would that replicate what you tried to do? I should be able to do that.... Hhm, no problem with that either.
I did discover that the 4 holes which are inside the rounded rectangle on the left side -- actually are 8 circles.
Are you able to make videos or animations? If so, and if the next time you work on the file, you see the same problem, would you make a video, so we can see what's happening?