Until 2004, a GP could remove a patient from a list without giving a reason, although guidance acknowledged that it was good practice to do so.
Some patients were unhappy that they had no warning and no opportunity to put their side of the story.
Under the NHS (General Medical Services) Regulations 2004, patients must be given a warning in the 12 months before removal.
The ombudsman's annual report, published last week, said: 'It is of concern that some patients are still being removed without adequate warning.'
Criticism included GPs relying on oral warnings without keeping written records or citing as a warning an event that happened up to seven years earlier.
Such complaints were the subject of 32 of the 139 cases against GPs settled in the financial year.
A total of 42 per cent of all cases were upheld in full or in part.
Acute trusts accounted for 309 of the ombudsman's reports during the period, 146 concerned PCTs and 75 mental health trusts.
Continuing care complaints accounted for more than half of the NHS work dealt with by the ombudsman and were recorded in separate figures. These showed that the ombudsman reported more than 1,300 such complaints in the period - 962 against PCTs, 362 against SHAs and two involving mental health trusts.