Councillor Angela O'Leary was concerned there was no message informing people that failure to tick either box would be taken as a 'yes' vote.
"I don't think when we went out with this question that this was implicit," Ms O'Leary said.
"To be statistically correct and to have some integrity in the question you can really only add weight to those who ticked yes to all nine projects."
In the analysis report a bar graph shows how many people ticked yes or no and another separate bar shows those whose votes were counted as a 'yes' by default (For example, 925 "not ticked implying yes" for the Central City park).
Councillor Leo Tooman said it was very dangerous to assume what people wanted.
"Just because you assume something doesn't mean they have said it. It is very dangerous," Mr Tooman said.
City chief executive Richard Briggs agreed with O'Leary and Tooman and told councillors to disregard the graph.
Ms O'Leary in a personal statement issued after the briefing said the overall analysis report was seriously flawed.
"The ratepayers of Hamilton have overwhelmingly rejected the mayor's budget and they have done this by abstaining from answering prescribed questions.
"That does not mean that you get to then interpret the absence of a no for a yes vote," Ms O'Leary said.
"I can tell you that from reading submissions one by one there is an overwhelming rejection against the mayor's Central City Park as an example, and yet the statistical data shows huge support for the project in the absence of 'no' votes."
In the analysis, certain projects that were not supported by the council's draft 10-year plan such as the library network plan and the original river plan have more support from the public than the nine projects listed.
Councillors were also informed that just under 20 per cent of written submissions to the 10-year plan had not been analysed by council staff.
They were told that 727 written submissions were in the form of hard copy submission forms and emails or letters.
Of these, council staff had not tried to incorporate the 416 emails or letters into the statistical report and have only included them in the non-answered forms.
Council general manager strategy and communication Sean Hickey told councillors elected members will be left to interpret messages that are not 100 per cent clear.
"If someone has said I think we should do option three, then we have included that in option three, but if someone has said I like the idea of option three, then we have not interpreted that into the statistics," Mr Hickey said.
Some councillors were concerned at that task but Councillor Dave Macpherson said one of the biggest arguments in the past has been staff's interpretations of the comments and that councillors were backing staff into a no-win situation.
