Investigating this question it seems Kyle Jones has the best answer and that out-of-universe it's sort of a plot-hole but, just for fun, some alternatives: Time continued to reverse during the commercial break so that Data may have expected that time was frozen at a different point than previously.
Let's break down the time points (the images at bottom may help).
- Troi, Data & La Forge transport to the Romulan Engine Room (images A & B below)
- They move into the singularity room and La Forge opens the compartment
- Data scans the singularity with his tricorder causing time to unfreeze and move forward at normal speed (for about 38 seconds)
- The Away Team moves away from the singularity to watch the engineers
- Cut to Picard watching the Enterprise explode and then time reverses again
- In the engine room the Romulans move in reverse, then "freeze" (reversing for about 10 seconds) (images C)
- Commercial Break
- The Away Team is back at the singularity
- The Away Team moves back to the engineering compartment where the alien is now standing in the middle (image D)
- La Forge notices the change and is in the process of asking Data when he is grabbed. Alien & La Forge fall to the floor (image E)
It's clear that none of the Romulans are in the same position from 6 (re-freeze) to 9 (Away Team re-enters the main compartment). Out-of-universe we'd simply say this is a poor edit (or poor continuity). However, in-universe we could say that there was, in fact, another time reversal during the unseen break (or time continued to reverse so slowly as to be imperceptible).
When La Forge is grabbed, it appears it is supposed to be the same time point as the initial transport, in which case it seems likely all of them should have noticed such a blatant change. They didn't though.
Some even more outlandish alternatives might be: (a) the subspace time disturbance for interfered with Data's positronic matrix so he didn't notice the very obvious additional Romulan or (b) Data's observational programming was unable to cope with the idea of time moving in reverse so it didn't automatically equate the first environment should correlate with the second environment (he would have had to "consciously" correlate the previously viewed scene with the current scene).
A. Shortly after transporting over to the Romulan vessel's engineering section:
B. Shortly after that (you can clearly see the 3 Romulans obviously present):
C. The moment time re-freezes, after time moved forward and reversed (just before the commercial blackout):
D. After the commercial break, they've left the singularity (after a short conversation with Captain Picard) and returned to Engineering where La Forge approaches the console:
E. Right after La Forge and the alien fall to the floor. The position of the other Romulans seems nearly identical to their position right after initial transport: