The deadline for applying for secondary school places is 31st October. Yes, parents have two months or more to apply before the deadline, but they can apply on deadline day if they wish. Personally I would advise against leaving it that late, but they are entitled to do so and they cannot be penalised if they do.
Local authorities must accept applications up to the deadline. If, say, a local authority chose to take its website down for maintenance on 31st October, they would have to allow those who had wanted to apply on that date to apply late and be treated as on time. Saying, "you could have applied earlier" won't cut it. The deadline is 31st October, not some random earlier date chosen by the LA.
If the problem was down to the LA or its suppliers, they should, in my view, treat applications from any parents affected by the problem as on time (provided, of course, the parents get their application in as quickly as possible). If the problem lies elsewhere (e.g. an ISP implementing an over-enthusiastic spam filter), the situation is less clear.
If the LA chooses not to treat the affected applications as on time and, as a result, children miss out on places they would have got, parents will be able to appeal. It will then be up to an appeal panel to decide whether the LA has acted reasonably.
I would recommend that the parents make sure that they have records of what has happened and, if the LA identify what went wrong, keep any information they get about that. If the LA agree to treat the applications as on time, they should get that in writing (email will do) and keep it so that they have evidence if the LA do something different.