Provided the appropriate security specialist confirms that the implementation of security measures has not been restricted due to the later stage at which their involvement was sought, i.e. everything that would have been recommended can be still be implemented, then the credits can still be awarded (provided all other compliance requirements met).
Considering the security requirements at an early stage of a project should ensure that the full range of security options is still available to the project, leading to the best solution. If advice is sought later but this does not restrict the options available, then the intent of the issue can still be met.