I think I understand what you mean... You're trying to 'clone stamp away' something, then your stamp source cursor reaches where you started painting over the thing you're trying to remove, and suddenly that thing (which by now is not visible on the screen) starts getting painted back in again?
I used to find this really annoying and ran into it all the time. Why it happens is perfectly natural - the clone stamp doesn't actually apply until you finish painting and release pen/mouse button - but I also always found it counter-intuitive and kept forgetting it would happen - after the thing is no longer visible on the screen I'd stop thinking about it.
The simple answer is to clone-stamp a little bit at a time when the source starts to get close to where you started - stamp a little, release, stamp a little, release.
Also, resample from different locations often - partly to avoid this, partly because otherwise if your clone-stamping catches up with itself you'll end up with a visible repeating pattern as you clone what you've already cloned.
If this is a big pain, sometimes it's easier to scrub away the thing you're trying to remove crudely (e.g. just paint it out), then refine that by clone stamping over that area: this way slight overlaps will be less serious. This also makes it easier to use less than 100% opacity with the stamp, which is a good idea for avoiding obvious repetition.
Switching between targeting one layer and all layers can sometimes also be useful.
