Server duplicates entities, then removes the duplicate, causing tick lag

When creating large amounts of entities, such as massive nether portal-based pigmen farms or placing armor stands/item frames, the server will occasionally duplicate entities and remove them in the following tick, causing tick lag.

Example Log entry, copied from my server console:
[03:05:24] [Server thread/WARN]: Trying to add entity with duplicated UUID d7a24a53-3d8a-48e0-a00d-7c169c42fe86. Existing minecraft:armor_stand#966, new: minecraft:armor_stand#966
[03:05:25] [Server thread/WARN]: Trying to add entity with duplicated UUID ba64bb14-491c-49b5-8e20-3f24d168bcd7. Existing minecraft:armor_stand#967, new: minecraft:armor_stand#967
[03:07:55] [Server thread/WARN]: Trying to add entity with duplicated UUID af1db051-cede-44ca-9785-6db65ec2474b. Existing minecraft:armor_stand#981, new: minecraft:armor_stand#981