While roaming through the 3.16 files, I've found the following issues and fixed most of them, or will be testing them to assure they're fixed before releasing a patch version.
Bug finds
bomber anti-sea promotion duplicated on bomber units (remove second, fixed)
air logistics listed twice in unit promotions (ranged/other, one at -10%, one -25%, removed -25% version, fixed)
supply 2 listed twice for air units in promotion tree (redundant, no effect, fixed)
coal production bonus from mine removed, but no other mines removed
conquistador upgraded to dragoon (should be lancer, fixed)
dragoon didn't upgrade to anything (fixed, set to tank for now, not landship)
hussar change to lancer (fixed)
UU knights/dragoons change unit stats not updated (fixed)
abbey+basilica reduce upkeep to 1 (abbey this is fine at 2) (fixed)
cothon?+barbary port doesn't improve sea plots like a normal lighthouse (fixed)
austria mountain troops strength listed as infantry (60), not rifleman (43), set to rifle + (fixed)
"text" for chichen itza uses pyramid effect (?)
Questions
fighter planes have no innate promotion vs air units (should be just reduced from default) (fixed)
wine/incense faith bonus are on shrine, not temple (intended?)
2 scientist slots + free science on babylon walls? (intended?)
candi has food (from garden) and 4 faith (from shrine) (intended?)
musketeer has FL bonus and strength bonus? (intended?)
Bug finds
bomber anti-sea promotion duplicated on bomber units (remove second, fixed)
air logistics listed twice in unit promotions (ranged/other, one at -10%, one -25%, removed -25% version, fixed)
supply 2 listed twice for air units in promotion tree (redundant, no effect, fixed)
coal production bonus from mine removed, but no other mines removed
conquistador upgraded to dragoon (should be lancer, fixed)
dragoon didn't upgrade to anything (fixed, set to tank for now, not landship)
hussar change to lancer (fixed)
UU knights/dragoons change unit stats not updated (fixed)
abbey+basilica reduce upkeep to 1 (abbey this is fine at 2) (fixed)
cothon?+barbary port doesn't improve sea plots like a normal lighthouse (fixed)
austria mountain troops strength listed as infantry (60), not rifleman (43), set to rifle + (fixed)
"text" for chichen itza uses pyramid effect (?)
Questions
fighter planes have no innate promotion vs air units (should be just reduced from default) (fixed)
wine/incense faith bonus are on shrine, not temple (intended?)
2 scientist slots + free science on babylon walls? (intended?)
candi has food (from garden) and 4 faith (from shrine) (intended?)
musketeer has FL bonus and strength bonus? (intended?)