But to make a set from the second and third cards a condition for the first (and second) cards must be met, so its not simply 2/49 and 2/48.

I just took a look at the link and the site writes 'Flopping a set or better (with a pocket pair) - 7.5/1 (11.8%)' There are 3 ways to flop a set or better,
event A - set from the first card = 2/50
event B - set from the second card = 48/50*2/49
event C - set from the third card = 48/50*47/49*2/48
Depending on the other cards that fall you may end up with better hand than a set
therefore the probability of hitting a set of better is event A + event B + event C = 11.8%

If you just want the probability of flopping a set, you must now subract the probability of making a boat or quads (0.74% and 0.25%), which can be calculated in a similar way. This gives the 10.8% for hitting a set.