What species of wood? Some species of wood do as you're describing, but others are less prone to it. How long did you have the wood and where did you get it from? I've also experienced this on newer-to-me wood from the big box stores, but it seems to improve the longer the wood sits in my wood pile. I suspect it's because the wood isn't dry enough.

Note that I tend to buy stain from whomever is closest and this is something I've observed across brands.