I cannot comment directly on the Eagle development product, but have some experience with the ExpressPCB. The errors I got mainly dealt with the schematic hookups (but the pcb layouts are a possibility also). Sometimes on a complex design, you need to zoom in on the designated areas and really look close at the connections. I had several points that were not 100% end to end connections. When you do your trace layouts, it is hard to determine the exact end point placements if you are zoomed out to far. Other possibilities are overlapping or crossing traces on the same side of the board. If possible, close the view for one side, carefully examine it for crossing paths, correct any found, the do the same for the other side layout.
Just a few thoughts.
Dialtone