There are duplicated airports at Barcelona (LEBL) and Girona (LEGE). Also LEGA, LEGR, LEZL, LERT, LETO, LEST and possibly others as well.

I also have this issue which seems to be persistent. The Valencia TMA as depicted by SD is different from the VAC chart (downloaded thru SD). The latter shows the Class D starting at various altitudes varying between 1000 and 4000 ft whereas SD shows a floor of 300 m (984 ft) throughout.