They look absolutely normal for a character grade floor. You have knots with dark mineral streaks (normal). You have splits in the wood. Both have been filled with appropriate colour. This is normal and what makes your floors unique. If you have ever split a cord of wood, you will know these are 100% authentic to the product you purchased.

There is no way to lighten them without ruining the floor. As a flooring professional I expect to see deep colour variations like this in a character grade floor. It is part of what makes these floors character grade. It's what rustic is all about.

These perfectly normal and perfectly random and perfectly coloured imperfections are what make this look real. In a vinyl floor or a laminate floor these character marks would repeat and repeat. Yours do not. That's how we know your floor is real wood and not something made to look like real wood.

They look great to me!

Thats how they are intended to look. Your floors are just fine.

Melanie, I'm currently having the same issue. I am having light engineered hardwood floors installed this week. The sample I looked at was uniform in color with no marks. Most of the floor is now in, and I came home and was surprised by the knots, scrapes and marks. I am going for more of a modern/scandinavian look, not rustic farmhouse. I actually thought one of them was a big scrape and tried to wipe it off. The one that really bothers me is the spider shape that looks like a kid drew on the floor. Of course the darkest marks are in highly visible areas. I asked about replacing a few planks but the floor is glued to the subfloor and it would be way too much work/damage to replace. I'm also wondering if I could somehow lighten some of these marks, with a light whitewash or wood marker...just so they aren't as noticeable.

They typically will only show the best pieces in a showroom sample board when they really should not. What is the flooring you purchased? And that is a natural part of the wood, you are not lightening that up effectively.