Q:

Pumpkin sprout and pepper plants have holes in leaves

I have a pumpkin sprout that sprouted very nicely, but I woke up this morning and the sprout had two holes in it.  The holes were yellowish and had scabbing around the outside.  The pepper plant is riddled with holes.  I'm not sure what the problem is and wanted to see if anyone else has had this issue. 

A:

If the holes are round, it may be flea beetles.   If the holes are irregular (and still in the middle of the leaf) it could be caterpillars.   You have to send pictures.   If the holes are round and cross-over the veins, it could be leaf-spot, a fungus.  Happening overnight rules out leaf-spot, I think.   
Normally, this is nothing to worry about.   It is, however, a great observation on your part!  Send pictures.   A little damage is not going to kill your plant.   It is a flag for you to start looking closer so that you can prevent irreversible damage.   Good for you! 
Thanks for the picture!  Based on what I can see I'd say earwigs could be your guest.  There could also be sawflies and slugs.   Can you see any slime trails?  You might have some bacterial damage as insects are good at transferring bacteria when they munch on your plants. 
Good news is that this plant will probably be just fine.   I'd scrape the wood mulch off my beds first thing as this provides good cover for earwigs.  Replace with well decomposed compost.  You shouldn't be able to see chunks of wood or anything you can recognize when you purchase bales of compost.   It should be dark, crumbly and smell like the earth.  Ask your nursery to open a bale for you to see, touch and smell.  You'll have to continually add it to the top as soil organisms will be going up to the top, eating it and then taking it back into your soil and pooping it out.   They will be mixing the organic matter into your soil for you.   Wood chips aren't decomposed so they can't be used this way.   Instead, decomposers are at work.   The problem here is they need nitrogen to do this work robbing the nitrogen your plants could use. 
As you scrape off this mulch look for insects.   This and going out at night with a flashlight can give you better ideas about who's coming to dinner.   Look under the leaves, around the roots (when they get older).   
Once you've checked out the insect population and made sure they aren't still near your plants, cover your seedlings with row cloth.   Bury the edges in the soil allowing some puffiness to allow for growth of your plants.   Sun and water get through this fabric well.  This will protect your plants from insects and slugs that aren't already amongst your plants.  
This little guy looks like he could benefit from some fertilizer as well.   Try fish emulsion.   It isn't very strong and I don't use it exclusively but like to give my plants a boost once they start showing nitrogen deficiency...the color of green is light or yellowish.   Water regularly, squash and pumpkin soils shouldn't dry out too much.  But do water deeply and try to not get the leaves wet.   Water earlier in the day so the leaves can dry off.  
It is ok to lift the row cloth to check your plants.   When they get bigger and begin to put out flowers the row cloth can come off.   Always keep vigilant for new or worsening problems.   Let us know what else you've found and how your pumpkins or other vegetables are doing.   No problem is too small!   A few holes and spots aren't going to kill your pmlants but are good indicators of problems that might...could you post a picture of your pepper plants?   
Update: Thanks for the pictures.  Same insects maybe more flea beetle on your pepper plant.   Where are these plants?   Do you have them outside in a garden?  Row cloth won't help at all unless all insects are gone.   Do get rid of the chunky mulch.   Add decomposed mulch to the top of the soil (good 1/2") around your plants and let's try 
diatomaceous earth on top of that.   I've never used the stuff myself.   But to discourage insects crawling around on your soil eating your plants this might just be the perfect solution. 
This is the equivalent to broken glass shards for us.   Clean off chunky mulch, fertilize with fish emulsion, apply 1/2" decomposed mulch and then apply diatomaceous earth according to directions.   Please let us know what you do and how it is helping, or not...OK?   More pics of your garden, please. 