Manhattan location—some might see this as a "pro," but sometimes the proximity to Penn Station/tourist locations in Midtown makes it hard to just get lunch or get to work on time
Not enough conference room space—a company undergoing rapid growth, of course, has these types of downsides. There's a daily fight for private space to conduct important calls/meetings in the New York City office. Luckily, that's not an issue in the CT office
IT moves slow—This isn't so much their fault as it is, I think, a lack of available specialized personnel at any given time.
Commuter benefits could be more robust—there's really only a pre-tax benefit available and I don't think it really helps much with the exorbitant MTA costs. However, this is typical for companies of this size in the US...