Yes, this is misconfiguration. Make sure mason-lspconfig is not setup before nvim-java. Use starter-kickstart project as a reference. If you can't figure it out, share your complete configuration.

I ended up doing this:

return {
    "mason-org/mason-lspconfig.nvim",
    opts = {
        ensure_installed = {
            "clangd",
            "lua_ls",
        },
    },
    dependencies = {
        "nvim-java/nvim-java" // Added this to make nvim-java load before mason-lspconfig.nvim
    }
}

Althought I don't know if this is the correct choice. This does seem to fix the error, but if there's a 'better' solution then I'd like to hear it.
My other plugins' config files are made of just the installation part. For example:

return {
    "williamboman/mason.nvim",
    opts = {},
}

That seems to have fixed the two signatures showing up.
However I'd like to remove the URIs shown in this screenshot (starting with "jdt://...").
I believe this is possible as the first signature in my previous screenshot did not show these, and they take up lots of space making the docs harder to read.

I'll start another discussion and mark this as solved in the meantime. Thank you for your help.