A lot of cheaper guitars will have multiple joined pieces for bodies. Its not uncommon for someone here to strip a body of its paint and find a 5 piece body.
There's also attention to detail. The routing job under a pickguard can tell you a lot. There can be 3 neatly cut spaces for specific pickup sizes, or there can be a swimming pool sized ditch carved out to accomodate any generic pickup combination.
Intonation, and overall measurements are something I've come across as well. Typically, a $120 squire strat will not intonate as well as a USA Fender or Japanese Squire will. Position markers can be slightly off, there could be knots in wood, the wood could be flatsawn instead of quartersawn for a neck, the quality of the hardware may be inferior, etc. .
For example, I just had a lower end LTD in the shop. The owner was complaining about tuning issues. I tuned it up, played a note and watched the note sink. So I restrung it. As I was restringing, I noticed that the tuning posts were wiggling a bit. So I tightened the nut on one, and the entire post snapped off and started spinning freely. These tuners were obviously not a quality product. I replaced them with some Gotohs, and everything was good.
Pickups are another one. I don't know much about them though, so I can't give you any indepth commentary about that. Im guessing magnets, winding and other stuff have to do with that...
There's lots and lots of little elements and cost saving procedures that can go into making a cheap guitar. There's lost of painstaking quality control and practices that make a great instrument.