@Nakanowatari
because many of the recent translated harem manga are isekai in which MC is either OP or has potential to be OP, and is more educated than fantasy world natives: so MC is more often misunderstood to be an ubermensch instead of a pervert.
Also the girls are
more perverted/ready for xxx with MC, because of either slavery, or the lack of reliable men in a medieval fantasy world.
Whereas, in modern day harems, MC is usually a regular guy so girls are
more critical of MC.
@Kingseeker
if you only mention when manga was published, then there are lots of new untranslated manga with pervert misunderstandings: so it's translators who are focusing on harems without the misunderstandings, not publishers.
Also, shinju absolutely is: the dwarf king thinks MC is a pervert. sheira (the mermaid princess) starts off thinking MC is a pervert
I can also mention other recent (translated) ones:
bokuben
Murenase! Shiiton Gakuen (not often but there are a few chapters like 35)
My love tiger: lolicon
High Risk Mission Therapy
Boku no Kanojo ga Majime Sugiru Shojo Bitch na Ken (many of the girls think MC is a masochist)
etc. etc.