Even though you have designed the model such that the input to the MATLAB Function block is a vector, you will receive this error message if Simulink cannot successfully propagate the signal widths to the MATLAB Function block input (in which case it defaults to a signal width of one). This can sometimes happen for MATLAB Function blocks that are inside a loop, where the output of the MATLAB Function block eventually feeds back to the input of the same MATLAB Function block.
Have a look at the attached example model ("example.mdl") to see a demonstration of this error message. To resolve the error, you need to add more information about the dimension of the signals in your model.
For example, in this case, you can do one of the following (this is not an exhaustive list of solutions):
1. Open the MATLAB Function block editor, and click Edit Data. Select the input variable "u", and set the Size to 3. See "solution1.mdl".
2. Place a Signal Specification block in the feedback path, explicitly telling the MATLAB Function block that this signal has a width of 3. See "solution2.mdl".