If you have taken damage or are low on weapons, when assigned a new mission it should be a return to base.
In the OP's case, it sounds like this was an ASW patrol encounter which would not have ended the current mission when completed and thus didn't give the expected return to base. So this might be an oversight where we may have to consider all engagements as a possible "end of current mission", if the player sub needs to return to base.
...or we leave it up to the player to do whatever they can to achieve their mission goals. Keep in mind that the OP may have had to return to base and fail the mission, but the tonnage they earned in that fight would offset this instead.
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