It is always best practice to leave space between your floors and rooms.
If you are creating two levels which share the same platform as floor and ceiling, and you try to give each one a different texture, you will have this problem. If you need a different texture for each, go down an extra floor so that there is a level between the two.
The same thing goes for walls. If you need a different texture on two walls that are back-to-back, create a hallway between them or otherwise leave a space between the two walls.
Also, not every floor or wall texture will have this problem. Some are closely enough alligned that you see no distortion. Sometimes, it can also be affected by your video card, depending on the chip type and amount of memory on board.
Hope that helps. Happy game making.
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