"a coffee" is the same meaning as "coffee" here. In the Chinese sentence there is no "一杯". Coffee is considered uncountable unless there is a specific amount specified.

"I'm having coffee with them in the office" is marked wrong.

'I'm drinking coffee with them in/at the office' should also be accepted, it is a more literal translation & makes sense in English

Normal English phrasings aside, isn't the construction "我和他们“ making the combined group the subject of the sentence? In which case it should be translated "They and I/I and they are having coffee at work." Translating "I'm having coffee with them at work" makes the other people into a modifier on the action, not active agents as part of the subject.

What is wrong with at the company?

Not at work, but in the office or company. Please review. Shall flag this issue.

好冷啊。。。