The InOdiham community group planted 10,000 bulbs on the approaches to Odiham as part of a project which had Hampshire County Council approval.
Dilly Howard of inOdiham said they were "really, really disappointed" to discover part of the area being dug up.
The group said Hampshire County Council apologised and said it did not know the bulbs were near the bus stop area.
More than 50 volunteers from the inOdiham group planted the bulbs as part of an effort to improve the look of the town's roadsides.
The group had applied for a licence to carry out the planting at a cost of Â£109.
Mrs Howard said she was pleased with the council's response and the group would plant more bulbs around the bus stop.
"Come the spring, it'll look lovely," she added.
Councillor SeÃ¡n Woodward, executive member for economy, transport and environment at Hampshire County Council, said: "I am sorry some of these bulbs have been disturbed for the new bus stop which is being put in place as part of the new development.
"We would be happy to arrange for some new bulbs to replace the ones which have been dug up."
Contractors have built a bus stop where volunteers had planted thousands of bulbs.