Utivich being captured is not shown in the film, but it's quite reasonable to expect. There're numerous high rank Germans in the theater, Hitler included, so it's only reasonable that SS, Gestapo and other Germans' services pay extra attention to anything around the theater and expect some kind of subversive act.
Now when Utivich and Raine are later interrogated by Landa the latter explains that he has thoroughly interrogated all the people whom Basterds have labeled with swastica and released and so he knows all the names and looks (to some degree of precision). Recall that near the beginning of the film - when Donny smacks one of the captures German soldiers - Raine calls several of the Basterds by names and so the surviving German soldier has chances to remember those. The German soldier is also not blindfolded and it's not dark around and the Basterds stay all around him and so he has good chances to see how they look like. There's good chance that the same setup repeated numerous times with different German soldiers and so Landa could have obtained enough details by interrogating them.