Extended work hours
I find this happening more that I would like. It's really important to create balance and unplug when you're not on the clock. It's so easy to find yourself hopping back on your computer after dinner to 'finish up a couple things'. If my weekends aren't very busy, I'll try to get ahead and get a few things out of the way so I can have an easier Monday or finish up things that I couldn't get to on Friday. If you let it, work will consume you. Before you know it, you're working 50 hour work weeks consistently.
Similar to working extended work hours, it's easy to become an over achiever if you weren't one already or become even more over achieving. More than ever now, your results are the proof of your productivity since no one can pass by your desk/office and see you working. Now, I feel more pressure to get things done and get them done quicker and more efficiently.
Other people sometimes don't understand the arrangement
Sometimes people think that because you work from home, you have tons of free time. In fact, I work more! I think it was Revanche who posted about having to deal with this a few months ago.
Spending too much time alone
It sometimes get dull sitting at home alone. There's no water cooler chats with co-workers. And while I'd like to work from coffee shops etc, if I get on my computer early and really dive into my work, the last thing I want to do is detach so that I can change locations and drive somewhere. Also, while I'd like a change of scenery more often, I don't find myself as productive if I work elsewhere.
There might be more, but that's all I can think of for now. Like anything else, there are always positives and drawbacks.