Many PCB software packages will mirror the bottom layers. Make sure when you are viewing the board, all layers line up. Eagle and many others will default to mirroring these layers - please do not.
I am confused by this. My experience with Eagle is that if you leave well enough alone, the layers matchup. Actually the top layer is what gets mirrored in production and the bottom layer is good as is. This is to insure the photo tools are “right reading emulsion side down”.
Eagle is not the problem - it is the default CAM files that Eagle provides. Many fab houses require the layers to be mirrored one way or another, other fab houses do not.