1) Beitzah 9 – the Mishna records a machlokes Bais Shamai and Bais Hillel whether a ladder can be carried from one bird coup to another. The gemara writes that the issur here is one of mar'is ayin because a ladder is used to repair roofs. Rashi (d”h haro’eh) explains that carrying the ladder gives the appearance that one is violating the issur of working on Yom Tov.
2) Krisus 21 – Even though there is no issur of eating the blood of a fish, the gemara says that it is prohibited to gather the blood in a cup to drink. Rashi (d”h she’kinso) explains that should someone see blood being drunk, he/she will come to the mistaken impression that it is permitted to drink any blood, i.e. even animal blood, which is an issur d’oraysa.
From these two snippits it seems that there are two different reasons for the issur of mar'is ayin: Rashi in Beitzah focusses on the onlooker having the misimpression that the person engaged in some act is violating an issur (see also Rashi d”h kol makom Avodah Zarah 12a “haro’eh choshdo b’dvar aveirah”), while Rashi in Krisus focusses on the onlooker him/herself perhaps being led to err in halacha based on what he/she witnesses. Interesting that the Badei haShulchun (Hilchos basar b’Chalav 87:4 Beiurim d”h Davka) cites these sources, but fails to mention another relevant case from Hilchos Basar b’Chalav:
3) Chulin 107 – One is not permitted to eat meat at the same table as someone eating a dairy meal. The gemara questions whether this would be permitted if the two eaters are ‘makpid’ not to share food with each other. The gemara answers ‘yomru kol hasrikim assurim u’serikei Baysus mutarim?’, an expression borrowed from Pesachim meaning that we do not distinguish between someone like Baysus who is a very fast baker and other people. Explains Rabeinu Gershom: it would not be apparent to an onlooker that the two people eating together are makpid not to share food, which would lead the onlooker to think it is permitted for any two people to eat basar b’chalav together. Rabeinu Gershom’s concern is not that the onlooker might think that the two people eating together are violating an issur, but that the onlooker him/herself will be led to violate an issur based on his/her misunderstanding the situation.
It seems to me that Rashi stressed the need to avoid appearing doing something wrong only where the gemara explicitly uses the phrase mar’is ayin. Perhaps one could argue that there are two types of issurim: a separate independent issur of mar’is ayin, which the sugya in Beitzah and A”Z addresses and which revolves around the doer becoming suspect of violating issurim, and cases like the cup of blood or not eating meat and dairy at the same table, which are just extensions of the larger issurim of dam and basar b’chalav and the issue of misunderstanding is just an explication of why Chazal extended these issurim so broadly.