This code strongly suggests that the problem is somewhere else in your code (something that you aren’t showing or even looking at):

defmodule Demo do
  def run(additional_on_clauses) do
    Enum.reduce(additional_on_clauses, true, fn {field, map}, query ->
      query =
        if Map.has_key?(map, "$in") do
          # dynamic([q], field(q, ^String_to_atom(field)) in ^map["$in"] and ^query)
          "#{field} in #{inspect(map["$in"])} and #{query}"
        else
          query
        end

      if Map.has_key?(map, "$between_equal") do
        # dynamic([q],
        #  field(q, ^String_to_existing_atom(field)) >= ^Enum.min(map["$between_equal"]) and
        #  field(q, ^String_to_existing_atom(field)) <= ^Enum.max(map["$between_equal"]) and
        #  ^query
        # )
        "#{field} >= #{Enum.min(map["$between_equal"])} and " <>
          "#{field} <= #{Enum.max(map["$between_equal"])} and " <>
          "#{query}"
      else
        query
      end
    end)
  end
end

data = %{
  "$additional_on_clauses" => %{
    "event_date" => %{"$between_equal" => [~N[2019-05-03 00:00:00], ~N[2019-05-04 00:00:00]]},
    "infection_category_id" => %{"$in" => [2, 3, 4]}
  }
}

data["$additional_on_clauses"]
|> Demo.run()
|> IO.inspect()

$ elixir demo.exs
"infection_category_id in [2, 3, 4] and event_date >= 2019-05-03 00:00:00 and event_date <= 2019-05-04 00:00:00 and true"

And to my earlier point changing to this:

data = %{
  "$additional_on_clauses" => %{
    "event_date" => %{"$between_equal" => [~N[2019-05-03 00:00:00], ~N[2019-05-04 00:00:00]]},
    "infection_category_id" => %{"$in" => [2, 3, 4]}
  },
  "$additional_on_clauses" => %{
    "infection_category_id" => %{"$in" => [2, 3, 4]}
  }
}

data["$additional_on_clauses"]
|> Demo.run()
|> IO.inspect()

has the following result:

$ elixir demo.exs
warning: key "$additional_on_clauses" will be overridden in map
  demo.exs:28

"infection_category_id in [2, 3, 4] and true"