Does it matter that I took the rubber off the needles for my samples during my SIBO Test?

No, it doesn't matter that you took the rubber off the needles for your SIBO (small intestinal bacterial overgrowth) Breath Test samples.

Removing the grey sheath from the needle doesn’t affect the breath gas levels in any way.

It’s just there as a safety device in case you put your finger in the needle holder.