Eagle question

An example it connected the +35v and the -35v together.

It will not do that unless it is by mistake connected somewhere on the schematic. Or maybe in Eagle it doesn't discriminate between a + or a - in a label. Rename them Plus35 and Minus35 and see what happens. If the errror stays, it is in the schematic.

Does Eagle have a Power supply configuratior (my CAD has). If so, check that they are not connected in the Configurator.

Are you have an opamp with mixed up power pin connections.
Don't look for an Eagle error, look for a schematic error.

Jan