Yes, definitely contact the court as soon as possible, and apologise.
In the notese section of the form,
http://www.hmcourts-service.gov.uk/cms/files/n 149_web_1105.pdf
it states that if the applicant is late in submitting the form 'the judge may make an order...[and]...can order...[the applicant to pay these costs].
So it's not definite that the court/judge will punish the applicant, but they can. So the applicant should contact the court ASAP and apologise for being late.