Desert temples and Jungle temples generated in WB loses their loot chests. Strongholds loses their hallway chests and their Silverfish Spawner.

Seems to be only old vanilla structures that uses a boolean check when generating the chests/spawners. now the question is, why is the NBT data they get saying the stuff is placed already when it actually isn't? hmm.

Related issue : TelepathicGrunt/RepurposedStructures#3

fixed in v1.3.1 which should be released shortly. Structures were added twice into the biome's feature list which caused them to be generated twice replacing themselves in the exact same blocks which made them look like they were generated once. For Desert temples, Jungle temples, and Strongholds, they have an extra check for if the chests and spawner was already made and if so, doesnt generate them. And since the structure was made twice, the second pass wouldnt generate the chests/spawners leading to this bug.

Fixing this bug has greatly improved worldgen time as structures are now made only once