I have a similar experience with your file, on the same kind of system, except with 0.48.4. What I experience looks exactly like what you describe:
The broken copy has one dot raised by a large distance and the other 99 lowered by the same.
But your 2nd screenshot doesn't seem to fit that same description. Maybe you accidentally inserted the wrong one, or something?? In the 2nd screenshot, it looks like a very narrow line/path is selected.
Couple of comments. The file shows the original circle (Ellipse) and only 99 Clones. It seems to me that it should have 100 clones along with the original. I don't know if missing one unit of the whole array would cause this kind of problem. It doesn't seem like it should

. But we probably should be testing with the whole array. Actually, nevermind. I just made up a quick 3 x 3 array in the same file (1 Star and 9 Clones) and tested, and it exhibits the exact same behavior.
And 2nd comment, for whatever reason, it's always the original that goes to the top, and all the clones are shifted downward. I don't know what significance that has, but it seems like it should provide some kind of info (for those who are more technically inclined than I am).
Someone else will have to address the technical aspects in the possibility of a bug. I do know of one bug which could be coming into play. I did the same test that I did in your file, except in a new blank document, that is set up to prevent that bug. It does NOT display that behavior. So I would guess that it is a bug, at least partially related to those transform attribute related issues we've seen so often (or at least I have). Whether this is a new "variety" of those, or whether it's exhibiting entirely known bug behavior, I don't know. I have seen tiled clones affected by this bug (and actually reported it a few years ago). But the part where it seems to be triggered by pasting -- that part is new to me.
I'm thinking it probably should be reported. Anyone else have any thoughts?
chrisjj, if I decide to report it, could I give them your file to test with?