Does the fact that the B and E strings don't sit flush in the saddle matter?

[Damani311]

I filed the bridge, but the strings still basically sit 50% out of the saddle groove. It's perfectly secure, but the B and E strings sit a few mm's higher than the other two strings.

Is this going to have any effect on sound/intonation?

[JustDavid]

If the strings don't move on the saddles when you play, I'd say it's fine.