I put all my fruit and vegatable scraps in my compost including seeds. This spring is my first time adding my own compost to my garden. Now all those seeds are germinating. I got a good chuckle but now I want to know what I'm doing wrong. I figure it's the obvious thing and I shouldn't be mixing seeds into my compost. Or maybe the less obvious that I didn't manage it correctly and the seeds weren't sterilized. Or something else entirely. What do other people do with seeds and compost?
If you manage your compost pile perfectly, it will heat up and kill the seeds. I've never managed my pile perfectly and there are always some seeds. Occasionally it's a happy thing -- last year we got a bunch of pumpkins from volunteer plants. Often it's a real pain: raspberry seeds left over from making jam are terrible; we don't put raspberry leftovers into the compost any more.
For the most part, though, I don't bother. A few stray cucumbers, pumpkins, or tomatoes aren't a big deal. They're not terrible to deal with like other weeds -- easy to pull out, they don't resprout, and they won't spread seeds (assuming you don't let them fruit). Sometimes you can get usable fruit from volunteers, but generally speaking I just pull them out.
It sounds like your compost isn't breaking down all the way.
Compost has to heat up and stay hot to kill seeds, and you need a full cubic yard or the pile won't really ever heat up. Even then, only the inside heats up -- you have to turn it periodically so that the compost on the outside moves to the inside where it can heat up, too. Our community compost bins are sometimes more than 100 degrees in the winter. It can be pretty impressive to see them smoking. Most household compost bins will never have the volume to get hot enough to kill seeds.
Worm bins don't heat up, but in a worm bin most seeds will sprout and get eaten by the worms -- same ultimate effect. Most seeds, but especially melon and squash seeds, are too woody for worms to eat until they've sprouted or decomposed so you'll also see them in the compost sometimes.
If you're really committed to seed free compost, let it sit for more than just one season, so it really has a chance to break down. Stop adding to the bin, leave it open to the sun and turn it from time to time (with a pitchfork or a compost crank), and start new pile for new waste. The seeds will sprout, but by turning them, you'll effectively bury the young plants.
You can also do lasagna beds in the early fall: put down a layer of mostly finished compost, top that with cardboard and top that with straw. The seeds will sprout but they'll be too hot and dark to survive, so they'll break down. By spring you should be able to dig the mulch in and plant the area without getting more volunteers.
If you somehow make all the compost pile heat up the heat will kill just about anything. However that is very hard - you'll have to thermally insulate the pile so that no parts cool down and the latter will almost likely mean the pile won't be ventes so you will get totally different chemical processes in there and the materials will ferment and turn into silo instead of rotting and turning into compost. So the bottom line is it's very hard to get all the seeds killed.
That shouldn't bother you. Unless you add some very active weed seeds in there removing those accidential plants is not a big problem.
As other people have said, I just chuck it all in. I get volunteer tomatoes all over the yard, and I'm OK with that.
I refrain from composting anything which I might spread by doing so - soursobs and couch grass suckers spring to mind - and anything with spikes (three corner jacks, rose and lemon tree prunings). Other than that, anything goes; let the seeds fall where they may.