This used to happen to me a lot on Nergal (I had 3 or 4 invisible probes at one point) but the invisible harvesters patch brought my probes back under control. It still seems to happen sometimes but the probes quickly come back under control so I think it's actually a separate bug I've seen...
Ships can appear twice (or more?) in the idle ships menu but only one of them will actually link to the correct ship and the extra ships will be invisible if you try to go to them. Once you've given an order to the idle ship then it's duplicates will also disappear from the list. This bug seems most prominent when there are multiple ships in a sector but it does happen to lone probes as well. For example earlier I built a colony ship and two outpost ships and in my idle list it listed something like:
Code:
Location
Colony Ship x 1
Location
Colony Ship x 1
Outpost Ship x 2
Location
Outpost Ship x 1
Once I'd given orders to the three real ships, all five "idle" ships disappeared.