The issue is duplicate, perfectly coincident copper pads in the MSP2807 composite footprint, so it is not obvious from the image.
- The parent MSP2807 part adds logical through-hole terminal pads—shown as MH pins, with a 1 mm drill and 1 mm pad.
- Nested inside the part, the TFT header still contains its original physical pads at the same coordinates.
- When placed on a host PCB, the parent pads receive the host nets, but the nested header pads retain separate internal nets.
- Flux therefore sees two pieces of copper occupying the same location but belonging to different nets and reports nine overlapping-copper errors.
In short: this is a footprint/net-mapping problem, not an actual header-spacing or board-outline problem.
The proper correction is to have only one electrical pad at each header position:
- Remove or make the nested header pads non-electrical, leaving the parent terminal pads as the authoritative copper; or
- Map the parent terminals directly to the existing nested pads and remove the duplicate MH copper.
Do not suppress the DRC errors or simply assign overlapping pads the same net; that would leave a structurally defective reusable part. The screenshot cannot expose the problem because both pad sets are exactly superimposed.