Looks like your regex is doing something wrong. Instead of 
Pattern pattern = Pattern.compile("<a.+href=\"(.+?)\"");
Try:
Pattern pattern = Pattern.compile("<a\\s+href=\"(.+?)\"");
the 'a.+' on your first pattern is matching any character at least one time. If you intended to set the space character the use '\s+' instead.
The following code works perfect:
    String s = "<a href=\"http://nemertes.lis.upatras.gr/dspace/handle/123456789/2299\"/> " +
            "<a href=\"http://nemertes.lis.upatras.gr/dspace/handle/123456789/3154\" /> " +
            "<a href=\"http://nemertes.lis.upatras.gr/dspace/handle/123456789/3158\"/>";
    Pattern p = Pattern.compile("<a\\s+href=\"(.+?)\"", Pattern.MULTILINE);
    Matcher m = p.matcher(s); 
    while(m.find()){
        System.out.println(m.start()+" : "+m.group(1));
    }
output:
0 : http://nemertes.lis.upatras.gr/dspace/handle/123456789/2299
72 : http://nemertes.lis.upatras.gr/dspace/handle/123456789/3154
145 : http://nemertes.lis.upatras.gr/dspace/handle/123456789/3158