I had found that in conversations I initiated if I had sent accidentally as “group individual SMS” then later another as a proper “single MMS” that then when iPhone users replied they kept replying to wrong things (either to me individually or something like that). I tried to wipe out all my SMS databases on the phone, have them re-send a message and it was still messed up. The best I can gather is that it is something also on their side’s cache where iMessage is smashing together the individual SMS and the group MMS and when they reply they don’t know what they are replying to.
If I can sit side by side with them I am sure we would clean up the “mess” which MAY be from me giving the multiple individual group SMS and later the single group MMS, but it was (and is) a mess for this one group (my extended family unfortunately).
Others that I am added to a group conversation on I can then reply to and everything works correctly (from their standpoint and mine).
Maybe this is partly what you were describing?