Let's divide this into 2 catagories: a) Yesoma b) chatufa/ketufa
Yesoma: The problem of an amen yesoma is for a person who requires the bracha for himself, but doesn't hear the bracha and merely answers amen. he hasn't fulfilled his requirement for that bracha. Others are strict to not answer amen at any time you did not hear the bracha [Shulchan Aruch O.C. 124:8] (there are varying opinions about the circumstances of Alexandria)
In our case, the only issue is where you didn't hear the blessing.
Chatufa/ketufa: The problem here seems to be that you have an obligation to say amen to a bracha [Shulchan Aruch O.C. 216:2] and your amen is being said improperly [ibid. 124:8].
So the question becomes- is it an obligation to say amen to brachos not established by Chazal, or is it just proper? If the former, chatufa/ketufa apply. If the latter, you shouldn't be worse off than not saying amen at all.
Magen Avraham [O.C. 216:3] brings a Midrash that a person has an obligation to answer amen to anyone who prays or blesses Israel even without Hashem's name. He cites this as the reasoning to answer amen after the harachamans in bentching.
This seemed very strange since the obligation to answer amen comes from the pasuk of ki shem Hashem ekra, havu godel lelokeinu [Mishna Berurah 216:8 quoting Yuma 37], and here you are not mentioning Hashem's name. The Aruch haShulchan's language is [O.C. 216:1] "when they make a mi shebeirach for someone, it is proper to answer amen, and with this he fulfills the mitzva of v'ahavta l'reiacha kamocha, and there for we answer amen after harachaman(M"A sk"3)".
The upshot is, there may be a big difference between messing up an obligation to aggrandize G-d vs missing an opportunity to do the mitzva of v'ahavta l'reiacha kamocha.
