Probably in your testing you have had an error or other misstep along the way in which you have overwritten the file handle variable fid for the file while it was still open and so the fclose operation is not operating on the correct fid.
You're not testing the return of fopen so you don't know that it has succeeded or you may have multiple connections to the same file open simultaneously.
As Adam notes, use fclose('all') to get back to ground zero and all will be well again. And, add the error-checking... :)
ADDENDUM
There are some other useful options in fopen for diagnosing such problems as well...
help fopen
...
fIDs = fopen('all') returns a row vector containing the file identifiers of
all open files. The identifiers reserved for standard input, output, and
error are not included. The number of elements in the vector is equal to
the number of open files.
filename = fopen(fileID) returns the file name that a previous call to
fopen used when it opened the file specified by fileID. The output
filename is resolved to the full path. The fopen function does not read
information from the file to determine the output value.
...
