Quite a common occurance, doesn't look like it's caused by multiple overlapping sockets, I believe it's caused by something to do with this zone ordering stuff:
Zone center: (-12.0, 25.0), Sockets: [('JD_DATA', (27.0, 36.0)), ('GND', (27.0, 26.0)), ('JD_PWR', (-51.0, 36.0))]
Zone center: (43.0, -16.0), Sockets: [('JD_DATA', (33.0, -35.0)), ('JD_DATA', (57.0, -31.0))]
Zone center: (46.0, 21.0), Sockets: [('JD_DATA', (32.0, 31.0)), ('GND', (60.0, 11.0)), ('JD_PWR', (36.0, 7.0))]
Zone center: (2.0, -14.0), Sockets: [('JD_DATA', (-17.0, 1.0)), ('GND', (21.0, -29.0)), ('JD_PWR', (-13.0, -33.0))]
Zone center: (-32.0, -16.0), Sockets: [('JD_DATA', (-22.0, 3.0)), ('JD_DATA', (-46.0, -1.0)), ('GND', (-42.0, -35.0))]
Ordered zone center: (-32.0, -16.0), Groups: [[('JD_DATA', (-46.0, -1.0))], [('GND', (-42.0, -35.0))], [('JD_DATA', (-22.0, 3.0))]]
Ordered zone center: (-12.0, 25.0), Groups: [[('JD_PWR', (-51.0, 36.0)), ('JD_DATA', (27.0, 36.0))], [('JD_DATA', (27.0, 36.0)), ('GND', (27.0, 26.0))]]
Ordered zone center: (2.0, -14.0), Groups: [[('JD_DATA', (-17.0, 1.0))], [('JD_PWR', (-13.0, -33.0))], [('GND', (21.0, -29.0))]]
Ordered zone center: (43.0, -16.0), Groups: [[('JD_DATA', (33.0, -35.0))], [('JD_DATA', (57.0, -31.0))]]
Ordered zone center: (46.0, 21.0), Groups: [[('JD_DATA', (32.0, 31.0))], [('JD_PWR', (36.0, 7.0))], [('GND', (60.0, 11.0))]]
Quite a common occurance, doesn't look like it's caused by multiple overlapping sockets, I believe it's caused by something to do with this zone ordering stuff: