If you use /clone to replace a mob spawner with some other block, then the flame particles do not disappear.
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/clone ~ ~ ~ ~ ~ ~ <coords of a mob spawner>
There will then be ghost flame particles where the spawner was.

Actual command used?

The command I actually used was this:
/execute @e[name=RoomFinder,type=ArmorStand] ~ ~ ~ /clone ~1 ~-3 ~1 ~11 ~-7 ~11 1 1 1
This clones a room relative to an Armor Stand named RoomFinder into this little room down by the void. Sometimes this region contains a mob spawner, and sometimes it doesn't. This issue also only seems to occur when you are out of range of a mob spawner in the room, and then a new room is cloned over it. Upon approach, the blocks that were mob spawners (but are now something else) have the flame effect, but otherwise act normally. The effect seems to disapear when:
1. You quit and re-enter the world.
2. You unload the chunk with these ghost flames.
3. You place a mob spawner at its location and break it.
I hope that is enough information to test and confirm this annoying bug.

Is this still an issue in the current Minecraft Snapshot 15w47c or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.

This bug is much more vast but still the game in 1.10.2: MC-108681
Command used?