Contractors working on changes to Wakefield's Newton Bar roundabout cut down around a dozen silver birches earlier this month.
Although around 100 mature trees on the western side of the junction were due to be axed or moved as part of the works, the felled silver birches were not in that group.
Wakefield Council said that Hinko, the firm carrying out the job, was "deeply apologetic", though the contractors themselves have not publicly commented.
The Forestry Commission said it would investigate the incident, although it said its probe will centre around "Whether there has been a breach of the felling licence regulations."
Felling trees without the required licence carries a fine of up to £2,500, upon a Magistrates Court conviction.
Gary Blenkinsop, Wakefield Council’s service director for environment, Streetscene and climate change, said: "We have been notified by the contractor commissioned to deliver the Newton Bar Corridor Improvement Scheme, that a number of trees have been removed in error.
"The contractor is deeply apologetic and immediately presented a plan of mitigation, which the council is currently considering.
"Wakefield Council is not aware of any approach by the Forestry Commission, but we will assist them with any enquiries should they make contact.
"We remain extremely disappointed that the trees were removed and recognise the upset this has caused to residents and environmental groups.
"In addition to making the road junction improvements, we remain committed to restoring the Newton Bar site to a condition which improves biodiversity by the creation of a new wildlife area which benefits the local community."
Local Democracy Reporting Service