Roots dislike and avoid light, while many forms of bacteria, pests and algae, enjoy it.. you should always avoid using clear containers. It both invites problems, and inhibits growth.
Before someone chimes in: BadKitty is right. You can grow plants and they may even do well, but you're also inviting anything else that happens to be present in that soil an increased opportunity to photosynthesize. Why take the risk if it's easily solved with tape or paint?
Never had an issue with clear containers outside of extremely long term plants. In theory they could cause all sorts of issues, in practice it's fairly hard to achieve assuming the rest of your grow is rock solid. If you already have a marginal setup or have stressed plants though I'd avoid them.