First, prestige class are exactly the same as base classes in this regard. You would achieve the same effect by multiclassing to sorcerer as you do by multiclassing to master specialist.
What effect that is is up for at least some debate. There are two major, official approaches to handling this, plus a very-common houserule that gets at the heart of your concern.
The more simple approach, which I’ll call the “round first” approach, is to just read the numbers off the table and add them together. This does mean that you get +2 to your Will save when you take your first level of master specialist, yes.
I call it “round first” because the numbers in the table are already rounded down for you—a wizard gains ½ a point of Will save each level, but the table doesn’t show that at odd levels, it just shows a gain of 1 every 2 levels. Your base Will save from your wizard levels is really +3½, and master specialist really adds +2½ at 1st, but you round those down to +3 and +2.
The other, “round last” approach, also known as “fractional” as that’s what Unearthed Arcana calls it, requires dealing with those fractions. You add +3½ and +2½ and get +6. With respect to your concerns, this may look like it is making things worse, but consider poor saves: it is pretty common to play a 2nd-level barbarian/2nd-level fighter/2nd-level ranger (the base of a horizon tripper build). At 6th level, this character has two levels in each of the classes that all have poor Will saves, so +⅔ +⅔ +⅔. If you round first, that’s +0 +0 +0, when the lowest a 6th-level character should ever be is +2. If you round last, you get exactly that +2—which is the point, rounding last results on multiclassed characters more similar to single-classed ones.
However, as you note, this still results in the wizard/master specialist getting a Will save that is too good. An extremely common houserule—especially when rounding last—is to say that you can only get the +2 the first time you get a good save. So the fact that your wizard already got the +2 Will from wizard 1st means he doesn’t get it again at master specialist 1st, so +3½ +½, for +3 if rounding first or +4 if rounding last. Since +4 is what a 4th-level wizard would have, this is in my experience considered the ideal result. The skewed saving throws that come from rounding first and repeating +2’s are really bad for the game.
But all of this is up to the DM; you will have to ask them what rules your game is using, and all characters—PCs and NPCs—should use the same rules.