There certainly is a tension when you talk about setting up a right to exclude others from a market—essentially, if you constrain the concept of market to the market for your one little invention. There is tension between that and the idea of competition.
So, to the extent that you have problems in a patent regime where maybe there are too many patents being granted, or maybe they're overly broad, or maybe they're being bundled in certain thickets, you can see a situation where they could create a transaction cost, they could create a friction in the market, create uncertainty that leads to litigation, or extensive negotiations between parties.
All of the energy and resources that are driven into that are energy and resources that are not driven into making new inventions, and marketing and selling them.