If you load a world from an older save, it will cause some of the villagers to be invisible and not be harmed. The screenshot shows me trying to place a block where these 'invisible villagers' are.
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If this helps, here's the server logs.
[WARNING] Keeping entity minecraft:villager that already exists with UUID f4a59da5-b8d7-4728-8583-4346d88bdff1
[WARNING] Keeping entity minecraft:villager that already exists with UUID f4a59da5-b8d7-4728-8583-4346d88bdff1
[WARNING] Keeping entity minecraft:villager that already exists with UUID f4a59da5-b8d7-4728-8583-4346d88bdff1
[WARNING] Keeping entity minecraft:villager that already exists with UUID f4a59da5-b8d7-4728-8583-4346d88bdff1
[WARNING] Keeping entity minecraft:villager that already exists with UUID 0a16e781-8eea-4915-b24e-664f3feb1c70
[WARNING] Keeping entity minecraft:villager that already exists with UUID 219e5a60-a887-491c-9b59-2df6642b3690
[WARNING] Keeping entity minecraft:villager that already exists with UUID f4a59da5-b8d7-4728-8583-4346d88bdff1
[WARNING] Keeping entity minecraft:villager that already exists with UUID 219e5a60-a887-491c-9b59-2df6642b3690
[WARNING] Keeping entity minecraft:zombie that already exists with UUID b61ca58f-e324-4cb4-95e2-38cc729fe545
[WARNING] Keeping entity minecraft:zombie that already exists with UUID b61ca58f-e324-4cb4-95e2-38cc729fe545
[WARNING] Keeping entity minecraft:villager that already exists with UUID 219e5a60-a887-491c-9b59-2df6642b3690
[WARNING] Keeping entity minecraft:villager that already exists with UUID 62d40dca-2c2f-43a0-8377-5814524f7601
[WARNING] Keeping entity minecraft:villager that already exists with UUID 62d40dca-2c2f-43a0-8377-5814524f7601
[WARNING] Keeping entity minecraft:villager that already exists with UUID 219e5a60-a887-491c-9b59-2df6642b3690
[WARNING] Keeping entity minecraft:villager that already exists with UUID 62d40dca-2c2f-43a0-8377-5814524f7601
[WARNING] Keeping entity minecraft:villager that already exists with UUID 219e5a60-a887-491c-9b59-2df6642b3690
[WARNING] Keeping entity minecraft:villager that already exists with UUID 62d40dca-2c2f-43a0-8377-5814524f7601
[WARNING] Keeping entity minecraft:villager that already exists with UUID 0a16e781-8eea-4915-b24e-664f3feb1c70
[WARNING] Keeping entity minecraft:villager that already exists with UUID f4a59da5-b8d7-4728-8583-4346d88bdff1
[WARNING] Keeping entity minecraft:villager that already exists with UUID 0a16e781-8eea-4915-b24e-664f3feb1c70
[WARNING] Keeping entity minecraft:zombie that already exists with UUID b61ca58f-e324-4cb4-95e2-38cc729fe545
[WARNING] Keeping entity minecraft:zombie that already exists with UUID b61ca58f-e324-4cb4-95e2-38cc729fe545
[WARNING] Can't keep up! Is the server overloaded? Running 2695ms or 53 ticks behind
[WARNING] Keeping entity minecraft:zombie that already exists with UUID b61ca58f-e324-4cb4-95e2-38cc729fe545
[WARNING] Keeping entity minecraft:villager that already exists with UUID 7e102731-6e52-40a7-9112-4b2c09b7f2d3
[WARNING] Keeping entity minecraft:villager that already exists with UUID 0ad51371-6a78-4c5e-a697-4ef39e5e572b
[WARNING] Keeping entity minecraft:villager that already exists with UUID eff11b0c-3bb5-440d-b0b7-4537da27f888
[WARNING] Keeping entity minecraft:villager that already exists with UUID 460e0693-1750-4adf-a851-26977718b55a
[WARNING] Keeping entity minecraft:polar_bear that already exists with UUID 0de3cb66-7adc-4610-80c2-095d638f899d
PS: Only 4 villagers are visible.