Before Hugo leaves Foundry during Faceless' stolen object quest, the player can observe him talking to Anna at their house. This observation can happen long after the player learned that Cornell is in Core City (and maybe even after the player met him). However, after Hugo leaves, Anna's dialog makes it clear that he left together with Acid Hunters, which is impossible in this case. (Or in any case, because on the most obvious timeline all events involving Cornell outside Core City happen before the SGS tunnel is cleared.)
One easy way to fix this would be to change the story so that Cornell only tells Hugo where to go, but Hugo goes there alone some time after (yes, this makes Hugo look even more stupid, but he is already not the brightest; also this leaves open why Jacek would believe that Cornell indeed convinced Hugo to go, though this could be just a favor that Cornell could collect later only if Hugo indeed swallowed the bait). I believe this change would only require slight adjustment of Anna's lines.
Alternatively, Hugo can simply be made to never appear anywhere except the cave with Jacek during the quest. Anna's lines before the quest (when she is not too worried yet) still need some work.
