30d increments should have 6h sub-increments by default, I believe. The manual setting for sub-increment length gets ignored if it's above a certain threshold (100 sub-pulses per increment, I believe, with perhaps some exceptions for the 30d one).
As for the general topic of the post: Welcome to Aurora. That's unfortunately just how the game works, and you often end up with situations where enemies are right on top of each other if you don't select small increments carefully. Sometimes you just have no warning.
If you should have had detected them for three days already and it didn't interrupt, then my guess is you met them before (as the "new alien race" event interrupts) and didn't set them hostile. Neutral encounters don't trigger interrupts.