Why do I get large fractions, sometimes bigger than 80% of the electricity generated going to waste? It ususally happens when I have wind turbines in the generation mix?

HOMER will record excess electricity in any time step in which the electrical production exceeds the load and the surplus cannot be fully absorbed by the deferrable load or the battery bank.  So if HOMER is reporting a lot of excess electricity for a particular system configuration, it's simply because that system experiences a lot of such surpluses.

I suspect you are asking how HOMER could possibly choose a system configuration with a high excess energy fraction as the optimal or least-cost configuration.  There are many possible reasons for that, most relating to the limitations imposed on HOMER's search for the optimal system.  For example, if you specify a wind turbine that is so big compared to the load that even one turbine produces a lot of excess power, and then you let HOMER choose between installing one or two turbines, then you are guaranteed to get a lot of excess electricity in the optimal system configuration.  Even if HOMER would prefer zero turbines or a smaller turbine, if you do not consider those possibilities then HOMER can't choose them.

Another possibility is that you specify a large wind turbine and allow zero or more, but you impose a minimum renewable fraction constraint of 20% or something.  In that case, HOMER will be forced to install at least one wind turbine to meet the renewable fraction constraint, and that one wind turbine might lead to a high excess energy fraction.

It's important to note that even with a well-designed search space, HOMER sometimes chooses systems that produce excess electricity, and there is nothing wrong with that.  It may seem crazy to invest a lot of money in a system that spends part of its time throwing away electricity, but in fact it costs money to capture and store that electricity for later use, and the value of that extra storage may not justify the cost.  HOMER ranks systems based on net present cost, at it has no qualms about excess electricity.  It recognizes that there is no value to excess electricity, but it also recognizes the cost of avoiding it.  The reason we created HOMER was to analyze that kind of tradeoff.