The main issues here are that
- the tag descriptions don't give enough guidance (if any at all) on how a tag should be used
- most users don't really make a difference between the device (hardware) and the OS (software) ("I have a problem with my iPhone, not with iOS")
Unless you want to update all the relevant tag descriptions, update hundreds of questions and keep monitoring the site to ensure that new users use the proper tag I don't see how this is going to change. To be honest, I also don't see why this would be necessary as the current use of the tags more or less reflects what people are talking about if they have problems with their devices.
Also, from the tag description of iphone:
iPhone is Apple's smartphone line. This tag can include questions about hardware, software and accessories.
so at least in this case, using iphone for software problems is ok.