Because your count variable is being incremented in the outer loop which is running over a dir() list of all files (including subdirectory names and the two "dot" directory entries), not just over the *.png files.
If you're only worried about the single directory, you don't need (and don't want) the outer loop; just use
pngFiles=dir(fullfile(file_path,'*.png');
count = numel(pngFiles);
for i=1:count
delete(fullfile(pngFiles(i).folder,pngFiles(i).name);
end
But, you don't need to iterate over all files, simply
delete *.png
will do the trick in the current directory or
delete(fullfile(fullfile(file_path,'*.png'))
wipes 'em all out in the subject directory.
