I'm using an iPhone 4s. My phone is still on iOS 8xx and works fine. My wife's is on the latest (9.0.1) and has the same problem. Resetting the phone takes away the grey blob, but lifting it to her ear activates the "raise to speak" feature that creates the 0:00 bubble again. No option in messages to remove the voice text feature, no way to disable the lift to speak feature (that I've found). We do not use iMessage, SMS only. Tried turning off Siri, no luck. Next step is to roll back, but that's a pain. Fortunately I think our latest backup on her phone was still in the 8xx iOS.
Update 10/05/15 Just updated OS to 9.0.2 - same problem. Every fix that seems to make the problem go away (restart, reset, add subject line, remove subject line, update OS, etc.) is only temporary. As soon as the phone is lifted (to the ear) with the message app open the voice box returns again to obscure the text entry field. Need a way to disable "lift to speak" feature somehow. (Yes, have also disabled Siri).