When you set a scoreboard value to 0 in a command block, it doesn't register the command as succeeding(even when it clearly does succeed), and as such conditional command blocks or redstone comparators will not activate.

Example:

Create a scoreboard: /scoreboard objectives add Test dummy

Add a value: /scoreboard players set @p Test 100

Run this in a command block, with a conditional command block above it(conditional command block can have any command, ie. "say hi") OR a redstone comparator next to it: /scoreboard players set @p Test 0

In a regular minecraft server, the first command succeeds as normal, and the conditional command block activates as intended. In a spigot/craftbukkit server, the first command succeeds as normal, but the conditional command block above it does not activate. I tried the exact same world on both vanilla minecraft servers and spigot/craftbukkit servers - it always works on vanilla, always fails on spigot(tried a build for 1.14.4 as well, still didn't work), even on a server without any plugins.

There's 2 attached pictures - showing the setup and the commands inside the blocks. The first command block runs fine - but the conditional block above it doesn't run, and the redstone comparator doesn't turn on.