Nothing about a disguised doppelganger clues in adventurers that the creature's actually a doppelganger; such a tell would defeat the creature's purpose. However, even low-level adventurers have access to spells and special abilities that can detect a doppelganger.
The question says the spell detect magic is unavailable; I've included it here for completeness.
A doppelganger's change shape ability is a supernatural ability, which, despite not being subject to dispel magic, remains subject to detect magic. The caster of detect magic can identify a spell effect in place by making a Knowledge (arcana) skill check (DC 20 + spell level, in this case likely DC 22 for the doppelganger's change shape (alter self) effect). The spell alter self is dismissible, and a creature's refusal to dismiss an alter self effect because—I don't know—the creature says the effect's concealing unsightly scars from monster-fighting or compensating for a bad hair day or whatever is unlikely to carry weight for very long if the party suspects doppelgangers are about.
Another spell of the polymorph subschool
The GM may determine that discerning a doppelganger's presence using detect magic is just too easy, ruling perhaps that supernatural abilities can't be discerned by detect magic or that Knowledge (arcana) checks can't be used to determine supernatural abilities in place. (These decisions have no small long-term campaign impact, by the way.) In such a case, because the supernatural ability change shape "functions as a polymorph spell," the change shape ability is subject to the rules for the transmutation subschool polymorph, which says
You can only be affected by one polymorph spell at a time. If a new polymorph spell is cast on you (or you activate a polymorph effect, such as wild shape), you can decide whether or not to allow it to affect you, taking the place of the old spell.
Hence, the next easiest way for, for example, a cleric to detect a doppelganger is casting upon the suspected doppelganger the spell face of the devourer, a level 1 transmutation spell of the polymorph subschool, maybe followed by the spell detect magic and a successful Knowledge (arcana) skill check (DC 21) to determine a spell in place to confirm the face spell worked (although this should be obvious). However, identifying a spell in place can take as long as 3 rounds if the GM says the caster must wait until the third round of detect magic instead of being able to do so during the first. Also keep in mind that the caster knows if the spell's target fails the saving throw against the caster's spell. If the target's face does not go all Cthulhu and the target also didn't fail its saving throw, the target then has another polymorph effect that it's chosen to keep. Unless the creature has some plausible explanation for this (which it totally could—magic is weird), a doppelganger is a good (but not certain) bet.
The extraordinary ability scent
What I suspect most commoners do to avoid doppelgangers infiltrating their thorps and hamlets is train animals. Using the skill Handle Animal to teach an animal the trick detect—or pushing the animal to perform the trick untrained—should alert the handler of an animal that possesses the extraordinary ability scent to presence of something out of place. The scent ability allows the creature to "identify familiar odors just as humans do familiar sights," and the descriptions of the doppelganger, the supernatural ability change shape, and the spell alter self mention nothing about changing the doppelganger's smell. A loyal dog should alert its master to a doppelganger; a cat could alert its staff, too, if it felt like it. So could an orc or half-orc with the feat Keen Scent alert the party.
This is likely campaign-dependent. A GM may simply rule that changing appearance also changes smell. However, commoners in such campaigns remain at the mercy of the many, many creatures that can change shape.
Failing all this, the PCs could use the 2nd-level Clr spell reveal true shape, which doesn't change the doppelganger into its true form but layers a translucent illusion of its true form over its false one, leaving ignorant masses unfamiliar with magic perhaps doubting the caster's veracity. Nonetheless, the spell lets the PCs know the affected creature's a doppelganger, and that's the important thing. However, the spell reveal true shape is from an OGL adventure path (that is, the spell was originally for Dungeons and Dragons 3.5) and may be unavailable, making the 3rd-level Pathfinder-exclusive Sor/Wiz spell pierce disguise necessary instead.
Of course, the spell true seeing and everything that grants a like effect (like the navigator's eye) reveals a doppelganger, as will careful use of some let's-ask-the-gods spells (like commune and contact other plane).
"Seems too easy to detect a doppelganger then. How do they survive?"
The a-doppelganger-replaces-a-PC plot has been around as long as the doppelganger itself.1 Since most PCs don't go around suspecting their party members of having been replaced, the same hoary old strategy that's been around since 1975 still works today: pick off an isolated adventurer, replace the adventurer in the party, betray the party or lead it into traps, swoop remaining gear, repeat. This can happen anywhere, but it's most common when the adventurers themselves are isolated, like in a dungeon or wilderness.
In a large urban area, going around casting detect magic is probably frowned upon if not a cause for alarm, and fewer animals accompanying citizens means a decreased chance of accidental exposure. Further, a doppelganger can make city folks disappear easier because there's the much larger population to draw from. A doppelganger could live undetected its whole existence in the slums, the authorities blissfully unaware. An ambitious doppelganger, however, still must watch its step.
A revealed doppelganger isn't likely to be much more of a physical threat than any other monster, and maybe even less. What makes a doppelganger dangerous is all of the plans it's made and things it's done and gear it's grabbed and authority it's garnered before the PCs come along.
1 In fact, doppelgangers were so ubiquitous in adventure submissions that during the Dungeons and Dragons 3.5 era Dungeon magazine submissions guidelines forbade as a plot a doppelganger replaces an important figure. (Also forbidden were, for example, destroy an evil artifact and rescue a kidnapped princess.)