Disclaimer: This is more or less an updated/ worse edition of the error MC-123652 I reported earlier, however, with the exact commands being provided in a different scenario with similar issues. Note that the error stems from /scoreboard test functions failing to activate chain command blocks when the conditions of the test are satisfied so the rest of the commands don't work at all.

Overview: I was playing on my now expired 1.12 realm (same one in which the MC-123652 happened on) and I added squid missiles which cause a guardian near a squid to make the squid blow up. I was finished adding it and then an error similar, but not the same as MC-123652 happend. Just like the original error of this kind the machine worked properly for a while (like 1 hour) and then went of control.

What I expected to happen: squids would explode near guardians and the machine would work.

What really happened: an MC-123652 style error happened.

List of exact commands and command block states (all split rows have repeating command blocks at the beginning):
Scoreboard Objectives
/scoreboard objectives add SquidM stat.useItem.minecraft.snowball
/scoreboard objectives add SquidLaunch dummy
/scoreboard objectives add SquidCounts dummy

Command Chain one
/scoreboard players test @a SquidM 1 1
/execute @a[score_SquidM_min=1,score_SquidM=1] ~ ~ ~ /testfor @e[type=squid,r=10]
/execute @e[score_SquidM_min=1,score_SquidM=1] ~ ~ ~ /execute @e[type=squid,r=10] ~ ~ ~ /scoreboard players tag @e[type=squid,r=10] add Silo
/execute @e[type=squid,tag=Silo] ~ ~ ~ /testfor @e[type=guardian,r=20]
/scoreboard players set @e[type=squid,tag=Silo] SquidLaunch 1

Command Chain Two
/scoreboard players test @e SquidLaunch 1 1
/execute @e[score_SquidLaunch_min=1,score_SquidLaunch=1,type=squid,tag=Silo] ~ ~ ~ /testfor @e[type=guardian,r=20]
/execute @e[type=squid,score_SquidLaunch_min=1,score_SquidLaunch=1] ~ ~ ~ /scoreboard players tag @e[type=guardian,r=20] add Target
/spreadplayers ~10 ~ 20 22 false @e[type=guardian,tag=Target]
/execute @e[score_SquidLaunch_min=1,score_SquidLaunch=1,type=squid,tag=Silo] ~ ~ ~ /summon tnt

/scoreboard players set @e[score_SquidLaunch_min=1,score_SquidLaunch=1,type=squid] SquidCounts 1

Command Chain Three
/scoreboard players test @e SquidCounts 1 1
/kill @e[score_SquidCounts_min=1,score_SquidCounts=1,type=squid]
/scoreboard players reset @e SquidM
/scoreboard players reset @e SquidLaunch
/scoreboard players reset @e SquidCounts
/scoreboard players tag @e remove Silo
/scoreboard players tag @e remove Target

Score Setting Command
scoreboard players set @a SquidM 1

Thanks to this error my realm is broken.