Some games (those that have a border on left side of the screen - Megaman 3 for instance) show graphics on 0th pixel, which is kinda annoying as it clashes with the border). This only happens when you have bilinear filtering and fullscreen enabled.
FCE Ultra doesn't exhibit this behaviour, so it's prolly a bug in the filtering code. Or a feature.
It's easily remediable by playing with Video->NTSC/PAL Screen values, but still, would be nice to see it fixed.