Issue
In a Smart Campaign, you have a flow step with multiple Choice options in it. When the lead goes through the flow, only one choice option is applied.
Solution
This is the correct behavior for a flow step with Choices. When the lead goes through the flow step with multiple choices, only the first applicable choice will be used. The rest of the choices will be skipped, even if the lead qualifies for them. If you want multiple choices applied to the same lead, you will need to separate the choices into different flow steps.
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