AVR-Chat

> Turns out that Eagle will allow you to make a connection while laying
> out the PCB even if the schematic doesn't.  I've just recently
> switched to Eagle from Winboard so I'm still learning how it does
> things.

OH my that sucks enormously..

Look for a setting somewhere to prevent/allow/warn on design rule violations.
I use the old dos orcad, which I have set always to prevent violations.
I've only had what you describe happen once in more than 13 years
using this software.