Now, this is actually expected.
Scala Toolkit includes Munit, while the reproduction also imports ScalaTest.
As a result, there are 2 test frameworks on the classpath and Scala CLI doesn't know which one it should use.
You can state the test framework explicitly, like this:

//> using test.dep org.scalatest::scalatest::3.2.19
//> using toolkit default
//> using testFramework org.scalatest.tools.Framework

import org.scalatest.flatspec.AnyFlatSpec

class ExampleSpec extends AnyFlatSpec:
    "example" should "work" in { assertResult(1)(1) }

That being said, I would agree a warning should be raised in such a situation, possibly mentioning the test frameworks available in the project.

We should be able to use multiple test frameworks in a single target. Maybe we generate just one in Bloop config instead of both of them? Or is the test being run separetely without Bloop?

We should be able to use multiple test frameworks in a single target. Maybe we generate just one in Bloop config instead of both of them? Or is the test being run separetely without Bloop?

We don't run tests with Bloop.
Rather, we have a dedicated test runner module.

Actually... perhaps we could just run all the test frameworks we can find, unless a framework is explicitly specified.
I now wonder why the current implementation doesn't do that already.
Let me try some stuff.