Yes, limited companies will receive penalties for any late filing of accounts at Companies House. This starts at a rate of £150 and grows the longer that accounts remain unfiled past the deadline. If the same company files late accounts for two years in a row, the late fees are doubled. Director(s) of the company may also face prosecution as they would be failing what they are legally responsible to do. Any penalties relating to accounts money paid are not classed as significant accounting transactions, so such transactions will not affect your dormant status.