Here's an iMessage issue I've had for a while, but have only recently considered writing about: having two separate conversation threads with a single person. According to my iPhone, I have two dads and two sisters and I am engaged in scattered conversations with each of them – and while this may be true for some people, it simply isn't the case for me.
What my iPhone seems to be doing is separating messages to e-mail addresses and phone numbers, and treating each of them as different conversations, despite the fact that they're clearly assigned to a single contact. This isn't how iMessage is supposed to work. I'm supposed to see one conversation with my sister in iMessage, regardless of whether I message her e-mail address or her phone number.
I've already checked to make sure that people can reach me at my cellphone number and my e-mail address when they send me iMessages (Settings -> Messages -> Receive At), and I've also double-checked that this is the case for my sister. I've also tried resetting my iPhone, toggling iMessage on and off, and sacrificing a small animal in Cupertino's name, but nothing has worked. My only recourse has been to delete the conversation thread based on my dad's and my sister's e-mail addresses and then send a single text to their phone numbers. But this isn't so much a solution as it is me giving up and cleaning up the mess that iMessage has left me. At least there's only one conversation for each person now.
If you know of a fix for this issue, please speak up in the comments (preferably by just one name – I've seen enough duplicates for the next little while).