This will be definitively resolved at the Summit June 29-30 as it's prominently on the rules discussion list.
Personally I would say that the 25 is already bet and if the 25 is left in front of the player (not scooped up), the 500 is an overchip and is merely a call of the extra 25 of the BB. But we need an answer as to what happens when the chips are scooped then pushed out together in a "gesture" that can be construed as a raise. Is it a mixed-chip bet at that point and therefore a raise?
My answer at this point: We can get into trouble if 500 + a 25 chip already bet is a call in one situation but the same 500 chip + the same 25 already bet is a raise if only the gesture is different, without any verbal declare. I really feel this should be the same bet both ways so we don't have to parse gestures, and in that case, it would be a call both ways because adding a 500 overchip silently (to a chip already bet in front of you) when facing a 25 bet is a call.
That said, I would rule for a raise if the gesture was compelling that it's a raise such as an upward motion with the thumbs...... but merely combining the two then pushing them back out really doesn't reach that standard for me. What gesture does reach a clear raise? Well unfortunately that may be up to the TD at the time and per Rule 30 "it's the player's responsibility to make their actions clear"... if the player intends a raise but he doesn't make himself clear and the TD rules a call, then it's the players fault, we don't ahve to micro-parse every unclear utterance and gesture. If the player intended a call but he gets a raise ruling, again, it's his responsibility not the TD, he'll be more careful in the future.
As you say, to you this situation was "unclear", and my personal bias is that if it's unclear, in this situation it would be a call. I'm pretty certain there's a contingent who for good reason would tend to rule a raise here, so having this on the agenda at the Summit will give us a more definitive interpretation.