Never had this issue and I played a stealth run all the way through. In what region was this? If it's what I think then probably the ship section in the Caspian, though I should note that level is very much designed around light-manipulation so you might have had issues if you went in gung-ho. In fact I could see the previous Lighthouse section also having such moments towards the end. Also worth mentioning that I purposefully played it only at night with no ambient light & in HDR for maximum effect. Truly a delight!
Btw, if it is those moments I'm not sure the new RT would help as much given that it has a timed delay before enough rays accumulate.
F.ex. (sadly can't embed it):
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