1. Too many invalid patents are granted by Patent Offices. In the US 92% of re-examination requests are granted, of which only 22% have all claims confirmed. 67% require claims changes and 11% are completely rejected (from techdirt 20 Aug 12). In EPO oppositions, approximately a third of patents are upheld unamended, a third require amendment and a third are revoked completely.
2. Patent Troll/Non-Practising Entity (NPE). Patent trolls enforce patents against companies, but have no intention to themselves manufacture or market the patented invention. They apparently cost US bodies $29 billion dollars in 2011. They seem to operate mostly in the electronics/communications sectors.
3. Patent Offices often have substantial backlogs of unexamined applications. This allows applicants to keep broad claims pending creating uncertainties for third parties who cannot be sure what scope of claims will be granted.
4. Patents are too expensive to obtain. This favours richer organisations.