I have also had the same thing happen. In the Spring of 1930, The Canadiens played in both series, and though the Rangers won, 3-2, in one series, the Habs were credited with a series win after defeating the Maroons, 3-1, in the other. The playoff screen, however, showed the series score as, 1-0, for the Maroons. They "won" the semis against the Blueshirts, 5-3. The Finals never appeared, and when simming to June 30th, no GM points were awarded (I led the Rangers). Neither were the player awards. The Rangers were credited with a Stanley Cup in the team and league history on July 1, 1930, but not the GM.
The next season, Toronto appeared in both semi-final series, but lost them both. The Finals proceeded normally, and the GM points and player awards were awarded. The player awards for the "lost" season did not appear in the league history. I guess the loss of a probable Vezina will save me when Lorne Chabot's contract comes due.
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Actually, it'll be interesting to see if it continues. It's kind of a humorous glitch and makes you watch the other series with a keen eye when your team jumps out to lead on their twin-headed opponent.