When AFR chooses the tools, it selects them based on what the technology database assigns via the strategy chosen for that feature.
Within the strategy you can choose tools based on an equation to find the tool that would best fit the feature size, or by a constant tool type and size, or finally you can also set one specific tool for that toolpath alone, or tool assembly.
Most commonly, the tools will be chosen based on the math equation to find the best fitting tool based on the size of the feature.
To ensure your tools are being selected from the tool crib you created, open the tool crib tab and check off the "Tool crib priority" button and then the "Use tool crib tools only".
If both of these check boxes are selected and a tool is needed for a strategy that is not in the tool crib provided, the toolpath will not be generated.
It is in good practice to select only the Tool Crib Priority button as the Strategy will select from the tool crib assigned first, and if it cannot find the correct tool based on the database settings, it will select another tool in its place. It will show a small red exclamation mark beside these tools to let the user know this tool was not within the tool crib. At this point you can choose to add this tool to your tool crib, change the tool, or maybe change the geometry to fit another tool.