Here's an example.
Example? Only time I recall them being off were times when they were "supposed to be off." Unless you looking at the back of the nacelles which aren't quite as well lit as the sides of the nacelles.
And there are couple of shots like that in the episode. Even if it's the rear part of the nacelle, there is enough of it showing that the glowing blue effect should be noticeable.
I dunno, it MIGHT be the part of the nacelles that aren't as well lit. I'm pretty sure the engine and deflector lights were on the same lighting pass, if not then a missed pass is likely the result. IIRC when those ships approach it's got an odd "stiffness" to it like it's one of those "digital mattes" they did in the S1 set.