The only thing I can suggest is to generate a netlist from the schematic (Design -> Netlist for Project -> Wirelist, then look under "Netlist Files" under "Generated"). Inspect it manually to see if it matches what you think the schematic says. If it doesn't, the problem is on the schematic side, otherwise it's on the PCB side (which would probably indicate a problem with the design rules).
By the way, disconnecting a resistor doesn't necessarily flag an error (the "Connection Matrix" controls whether or not it does). It could be what you intended, the program can't read your mind. Sometimes I place uncommitted components on PCBs for later tests or modifications. The program is only really at fault if the PCB doesn't match the netlist. So try generating a netlist, which should tell you if the problem is on the schematic or PCB side. If on the schematic side, look for a problem with a footprint or the way you're wiring it up. If on the PCB side, look for a problem with the design rules (which there shouldn't be unless you changed them).