1. It's heavy. In fact it's so heavy that it's sometimes (mostly? don't have a source at hand) more environment-friendly to reuse plastic bottles than driving all that weight around. Obviously, the weight also makes it inconvenient, e.g. if you don't have a car you have to put that on your bicycle and/or lift it to the next public transit station.

2. It can break more easily. If it breaks, you can cut yourself on it. You can also cut others which is why those bottles are prohibited at some places with security controls or some workplaces.

I don't think I'd work at a place where they think that my glass bottle is a deadly weapon. That sounds like a bad place to work.

The reason glass bottles are prohibited at some workplaces are mostly because of situations in factories(or similar) where you let your bottle fall to the ground and the glass can hurt others unintentionally, disrupting the work, (maybe also insurance, I don't know), etc. It's just to prevent workplace injuries.

I could have made that clearer in my sentence, sorry.

Um, right, which place would that be that you control the actions of others? I've seen two programmers get in a fight before, in a place I would consider rather safe and non violent.