Because Primordial is, as written in the rule books, a series of mutually intelligible but distinct languages – much like the range of how Portuguese speakers can understand Gallego speakers but may trip up with Spanish, but Gallego speakers can understand both, but not Catalán (which Spanish speakers will be able to "get"), while Catalán speakers understand both Spanish and Occitan (Provençal), but Spanish speakers don't really understand Occitan, and so forth. Primordial is separated into Ignan, Terran, Auran, and Aquan, and while they all can understand each other, they aren't the same language.
Thieves' Cant differs from guild to guild. The signs and symbols are ultimately mutually intelligible, but there will be some unique elements between different organizations. This is important to prevent against rival guilds. It makes a lot of sense that Scouts use a very similar but different language of signs, signals, and code words, just as assassins and bounty hunters and pirates and police watch investigators would all learn similar types of languages, with large overlaps. The more basic symbols would ring true across each, but all clandestine organizations would want their own symbols and signs, even within a sub-group of Rogue like assassin, bounty hunter, scout, thief, etc.
The Rogue PC should NOT be surprised when he or she encounters a rival guild's symbols and the DM tells him or her that it's a symbol the Rogue is unfamiliar with, despite knowing Thieves' Cant. What the Rogue PC SHOULD be surprised at is if every time Thieves' Cant should be relevant, the DM is saying it's mutually unintelligible. That's a bad DM.