A You first need to ascertain the extent to which your colleague's perception would be true if a disinterested observer were watching. Is there any other adult who might be able to confirm this? If not, you need either to try to observe the classroom dynamic yourself or, if this is difficult, ask for specifics.
If you decide the subject teacher is negative, you should ascertain whether it is because of a personality clash or concerns about your colleague's work, or because the presence of an assistant in the classroom is deemed unwelcome, irrespective of the individual's personal qualities and skills.
Some teachers feel vulnerable being observed on a daily basis and may prefer that no other adults are in their classrooms. Some are also unsympathetic to children with special needs who do not appear to have incapacitating difficulties. In some cases, teachers do not consider the assistant to be helpful to the child, who they may feel is made over-reliant by excessive adult support and guidance.
Teaching assistants can also cause problems by failing to understand classroom dynamics, distracting the class, unsettling the class's natural disciplinary patterns, or by failing to accept that the teacher is ultimately responsible for the operation of the lesson.
Resolving these issues is a difficult task, requiring much sensitivity and tact. This is made even more complex where those involved do not recognise the Senco's responsibility for resolving such difficulties. Hopefully, this is not the case in your school.