This bug only seems to happen when I run an execute command twice in a commandblock.
For example if I have a pig named Bacon:

execute @e[name=Bacon,type=Pig] ~ ~ ~ detect ~ ~10 ~ minecraft:air -1 say I love bacon

This command works, however when I use:

execute @e[name=Bacon,type=Pig] ~ ~ ~ detect ~ ~10 ~ minecraft:air -1 execute @e[name=Bacon,type=Pig] ~ ~ ~ detect ~ ~10 ~ minecraft:air -1 say I love bacon

Then the command fails. (this last command works in vanilla minecraft)
I'm only running Spigot, there are no other plugins involved.