"Now, the two structure arrays are identical. "
Sure.
"But, when I use "isequal" to compare x.name and y.name, it gives logic 0 output, although they are identical."
Sure. Because with your syntax you are not comparing those structures.
"Is this a problem in the function "isequal"?"
Nope, it is a problem with your code. The cause is very simple: this syntax
x.data
x.name
x(1).data, x(2).data, ..., x(end).data
x(1).name, x(2).name, ..., x(end).name
which means your code is exactly equivalent to this:
isequal(x(1).data, x(2).data, ..., x(end).data, y(1).data, y(2).data, ..., y(end).data)
isequal(x(1).name, x(2).name, ..., x(end).name, y(1).name, y(2).name, ..., y(end).name)
which is thus equivalent to this (using your example data):
isequal([1,2], [1,2], [1,2], [1,2]) % all equal -> true
isequal('name1', 'name2', 'name1', 'name2') % all equal -> false
which according to the isequal help, " tf = isequal(A1,A2,...,An) returns logical 1 (true) if all the inputs are numerically equal." Are all of your multiple inputs numerically equal? In the first case they are, thus the true output, in the second case they are not, thus the false output. Thus there is no problem with isequal, it is doing exactly what it is documented to do.
To learn more about comma-separated lists:
"And, what can I do to compare x.name and y.name correctly?"
You can resolve this by putting the fields into one array, e.g. a cell array as jonas showed, or by simply comparing the complete structures.
