A small company means that there are probably limited opportunities for advancement (unless new positions are created).
Sometimes you feel a bit "thrown to the wolves" to fend for yourself so you do not always know what to do, even in training. Would be better if there was more opportunity for hands-on training where you could shadow another person.
With multiple locations, you may not work in the same office as your boss, so it can sometimes be difficult to connect and get feedback/responses/meetings.
Sometimes there seems to be a struggle between the way things have been done in the past and new ideas.
Not enough paid holidays