I have see this myself, but only under specific circumstances, namely travelling at ultra-high speed.
There is a quirk of the game that causes this if you turn through 180 degrees at very high speeds. Doing this leaves the ship travelling
in the same direction it was, but facing backwards, and the exhaust appears to come from the front of the ship as it points away from the direction of travel, not the back of the ship. Indeed if you do a 90 degree turn and use external views, you can see the exhaust pointing up or down!
This will not happen in the normal game and therefore suggests that you have some OXP related issue, specifically relating to the ship travelling at ridiculous speeds.
(This is one reason I have an un-released 'Turbo-Boost' OXP sitting on my computer

)