Real time clock loses SCL I2C signal when backup battery is added?
When placing the battery, its body can be shorted to one or more vias. Or its placement can cause the holder to deform and short vias.

A quick fix could be placing some Kapton tape or other insulating material on the PCB.

A way to help prevent this from happening during design is creating restricted areas for vias/pads/traces on the package, so DRCs should warn you:



p.s.: apparently DRCs will ignore manually placed vias conflicting with vRestrict, so for manually placed vias you need either tRestrict or bRestrict. It seems that vRestrict was intended for the autorouter.