I think there are two problems here: First is that you are making an electrical connection through the resistor in your "connect" line. For resistors and other devices, you want to keep the "resistor" layer unconnected from its contacts. Otherwise, both terminals are on the same net and magic can't identify the individual terminals. The second problem is that you have a poorly defined resistor area. Your resistor wraps around the contacts, which makes it very hard for the extractor to determine where the resistor actually is. The way such resistors are usually defined is to define a resistor area that is rectangular and stops at the contacts. Assuming this is a diffusion resistor (if it's poly, same thing applies, anyway), you would want to paint "resistor" in the middle, up to the contacts, and paint "diffusion" around the contact. In that case you'd probably not want to define a resistor contact but just define a diffusion contact.