As @FumbleFingers says they all mean the same thing really, but they imply different amounts. All over usually means everywhere, so that has more of a sense of covering the floor - probably not literally in this case, but definitely making a mess!
On doesn't really imply any particular amount. It could be a little, it could be a lot, you just know that coffee was spilled.
Personally I don't hear over used in this way very much (on its own, as opposed to all over), but it has the same sense of being spread out a bit, instead of being in one place - just not as much as all over. Over can also mean "over the edge of something", which doesn't apply to the floor, but it might for "over the table" or "over the balcony".