A common issue for new XR650R owners is threading the dipstick back into the frame after checking the oil level. The shape of the dipstick makes it very tricky to line up the threads properly, and many new owners will cross-thread the dipstick.
One tip is to make sure the dipstick is angled slightly towards the right side of the frame when dropping it into the frame. This will help quite a bit.
Another option is to trim and inch off of the bottom of the dipstick. This will prevent it from interfering with anything inside the frame when inserting the dipstick.