As a former public servant and former secretary to the Armed Forces Council, I can tell you that we had problems in two areas. As I recall, the first problems date back to 1986-87, when there were drastic cuts to the administration. We simply lost all the administrative staff that archived documents.
For files prior to 1990, the National Archives' records are usually very complete and well indexed, which facilitates research. Things have changed since then because the centralized document control services in the large departments have disappeared, roughly at the same time as email came along. I would say it has become a free-for-all. The measure of control and the ability to access certain information on request depends on the file, the department, and the branch.
I think that the government as a whole and the various departments are trying to put some order back into things, but it is time-consuming and difficult. It also requires financial resources and significant information technology. The documents we receive under access requests vary accordingly. In some cases, we receive what we expected. In others, it takes a long time, and in others still, there are gaping holes because the files have not been retained.
I think this is a 21st-century problem. It derives from the great volume of communication by email and similar tools. Sometimes unexpected finds turn up in an email exchange, which surprises everyone, and the departments probably as much as us.
There is no obvious solution. I keep current on the various procedures the government uses to try to keep things under control, something that it has an interest in doing. Its attempts are full of pitfalls, however, and it is very painstaking work.