Apocrypha had very similar abilities to her original - flight, strength, and invulnerability. While it is not directly showcased it can be presumed she also has her sources Thinker abilities.
Like Alexandria, her power didn't defend against abilities that made heavy use of inter-dimensional phenomena, such as Scrub, Damsel of Distress, Foil, or March. Eidolon made use of this vulnerability to destroy her.
Unlike other clones she was not explicitly described as malformed in any way. Apocrypha was outfitted with a white costume of reverse coloring to Alexandria uniform with a broken tower in place of the originals whole one.
↑Rebecca Costa Brown Alexandria Invincibility via. body in stasis, flight and vastly enhanced strength, with perfect eidetic recall and consequent mastery of many skills Protectorate/Cauldron Brute Mover Thinker - Parahuman List, bolded edit by Wildbow.
↑HamiltonsGhost: Obviously we don't know the mechanics of Alexandria's powers, but I have always guessed that it was some kind of interdimensional or multi-dimensional attack. Not that I have any evidence, but the all-powerful nature of Sting combined with the fact that all powers are cross-dimensional in nature to some extent (because the power source/computing substrate is in another dimension) makes me think that it had to be something like that.
Wildbow: This would be an accurate guess, though the bit in brackets is a little off. The likes of Scrub, Damsel, Foil, or March would be able to damage Alexandria. - Wildbow on Reddit