Don't be confuse between the distance unit "pixel" (which is a number for the computer, and like real distances, is not bound to integers) and the entity "pixel" (which is a small dot to render the screen that can be colorised), nothing smaller than a pixel will be rendered precisely sure, but your computer should do interpolations to colorise the area clearly enough (a 5x5 square can be placed at exactly a 5x5 space pixels, but it may also be slightly off, the program will then decide what to do for that, does it draw it at integer positions only, or does it renders it with smoothing on the edges, or even other things).
The logic of your game can have half pixels, the drawing part have to compensate, it won't throw a "wtf subpixel what are you doing dude??! U crazy!" Error, it will just renders it in a certain way.