I know some teachers have used larger cards than what is suggested in the directions. It seem the kids do a better job when they have a larger rectangle show the fraction pictures.
You might also be right that the students might need some more fraction knowledge development if it's their first year experiencing curriculum like Investigations.
How have the students done with the other fraction activities up to fraction fish?
What fractions seem to be the most difficult?
My gut feeling is that circles will not help the students develop equivalence understanding any deeper or better than the rectangles.
If you share more about the confusions your observing, the readers on the list might be able to make more specific suggestions and recommendations. I think the confusion could be caused by a number of things. Some times they get better just through experience with the activities. Fraction Fish should be played regularly.