Let's say you get 2 different 1x100 scores. On the first score, you got the 100 on the first circle. You would've been at x0 combo (assuming no sliders or spinners) for this circle, meaning that it would've given you 300 points if you got a 300.
Lets say, on the second score, you got 100 on like, the 50th circle. You would've been on x50 combo, meaning that getting a 300 would've given you 50x300 points (15,000), but instead, you got 50x100 (5,000), meaning you missed out on 10,000 points instead of 200, making a score lower despite the same or higher accuracy and even combo in some cases.
(Edit: Don't know the exact formula for score from individual notes, this is just an example)
Basically, 300s later on in a combo are more valuable than 300s earlier in a combo.