The short answer: Not only is it OK, it's actually desirable.
Not that the lumps themselves are desirable. But they're a side effect of what IS desirable, which is not overmixing your pancake batter.
It all comes down to gluten.
Gluten is the protein in wheat flour that gives baked goods — everything from breads to muffins to pizza to pancakes — their structure.
The more you knead the dough or mix the batter, the more those gluten molecules develop. And the more they develop, the tougher and chewier your finished product will be.
Sometimes, like with a pizza dough, that's exactly what you want. But with things like muffins and pancakes, that's pretty much the last thing you want.
If you've ever had pancakes that were tough and rubbery, it's because the batter was overmixed.
To avoid that, you want to mix your pancake batter as little as possible. Just enough to incorporate the wet ingredients into the dry, but not long enough to break up all the little lumps. I like to say ten seconds as a maximum, but an extra second or two isn't going to make a huge difference.
And by the way, I'm talking about very gentle mixing with a wooden spoon. Not ten seconds in a blender or ten seconds of furious whisking.
Once you have a liquid batter, but still see plenty of lumps, you've mixed enough.
But that doesn't mean you want your pancakes to have pockets of dry flour in them.
So here's the secret: Once you've mixed up your batter, let it sit for 15 minutes. Either in the fridge or on the counter is fine. This allows the glutens time to relax, which will make the pancakes more tender, but it also gives those lumps a chance to dissolve on their own.
You'll see some bubbles at the top of the batter, which are caused by the baking powder releasing some of their gas. Totally normal. Also, if you're incorporating blueberries or some other ingredient into your pancakes, wait to fold them into the batter until after the resting time.
You can rest your batter longer, but you don't want too much of that gas to escape.
Resting the batter won't cause the lumps to disappear entirely, but the ones that remain will be moist enough that they'll dissolve during cooking, and you won't see any pockets of dry flour in your finished pancakes.
And by not overmixing, your pancakes will be tender and fluffy every time.
Also see: The Science Behind Fluffy Pancakes