One of the main amendments came from Robert Brown, Liberal Democrat convener of the Scottish Parliament's education committee, which succeeded in extending parents' right of appeal to the new tribunal system.
The Bill in its original form had restricted appeals where parents had been unable to resolve a dispute with an authority to those whose children had a co-ordinated support plan.
Mr Brown's amendment widens this to give tribunal access to parents of youngsters who have complex and multiple needs but do not qualify for a CSP. The plan is intended for those whose special needs require co-ordinated help from agencies outside the school.
The change has been welcomed by some organisations but is likely to face opposition from MSPs. Rhona Brankin, the former minister who sits on the Parliament's education committee, warned of "using up resources that should be made available for improving the education of young people".
Recourse to a tribunal would be a sign of failure, Ms Brankin said, particularly since the Bill provides mechanisms for mediation and disputes resolution.
Another potentially signficant amendment allows a proposed CSP to be dropped if authorities can convince parents that one is not needed. It was moved by Euan Robson, Deputy Education Minister, and thought to have been inspired by the Convention of Scottish Local Authorities which has been concerned about the costs of the legislation.
Ms Brankin, a former lecturer in special needs, is also a critic of this measure which she believes may disadvantage less well-informed and persistent parents.
"If authorities can claim that their provision is adequate without a co-ordinated support plan, as this amendment allows, then what is the point of legislating for CSPs?" she asked.
Cosla officials were still digesting changes to the legislation as we went to press, but said they are "generally positive, although our concerns about resources remain".