This is mule 3.9 rate throttling policy, it includes an after tag to enforce actual updating of the message store.

RateThrottlingPolicy.xml

<?xml version="1.0" encoding="UTF-8"?>
<policy id="67891011"
        policyName="RateLimitingPolicy"
        xmlns="http://www.mulesoft.org/schema/mule/policy"
        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
        xmlns:mule="http://www.mulesoft.org/schema/mule/core"
        xmlns:spring="http://www.springframework.org/schema/beans"
        xmlns:scripting="http://www.mulesoft.org/schema/mule/scripting"
        xmlns:api-platform-gw="http://www.mulesoft.org/schema/mule/api-platform-gw"
        xsi:schemaLocation="http://www.mulesoft.org/schema/mule/policy http://www.mulesoft.org/schema/mule/policy/current/mule-policy.xsd
            http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-current.xsd
            http://www.mulesoft.org/schema/mule/core http://www.mulesoft.org/schema/mule/core/current/mule.xsd 
            http://www.mulesoft.org/schema/mule/scripting http://www.mulesoft.org/schema/mule/scripting/current/mule-scripting.xsd
            http://www.mulesoft.org/schema/mule/api-platform-gw http://www.mulesoft.org/schema/mule/api-platform-gw/current/mule-api-platform-gw.xsd">
            
  <spring:bean id="cacheEmailRateLimiting" class="net.sf.ehcache.Cache" init-method="initialise">
      <spring:constructor-arg name="name" value="cacheEmailRateLimiting" />
      <spring:constructor-arg name="maxElementsInMemory" value="1" />
      <spring:constructor-arg name="overflowToDisk" value="false" />
      <spring:constructor-arg name="eternal" value="false" />
      <spring:constructor-arg name="timeToLiveSeconds" value="60" />
      <spring:constructor-arg name="timeToIdleSeconds" value="5" />
  </spring:bean>
  
  <mule:processor-chain name="notAllowedToPass">
    <mule:set-property propertyName="http.status" value="403"/>   
    <mule:set-property propertyName="Content-Type" value="application/json"/>  
    <mule:logger message="Calls Rejected as limit is reached" level="DEBUG"/>
    <mule:set-payload value="{&quot;message&quot;: &quot;maximum calls reached, subsequent calls would be rejected.&quot;}"  />
  </mule:processor-chain>

  <before>
    <scripting:component>
      <scripting:script engine="Groovy"><![CDATA[
                import org.mule.api.config.MuleProperties;
                import java.util.Map;
                import net.sf.ehcache.Element;
                import org.mule.api.transport.PropertyScope;
                import com.mulesoft.gateway.policies.PoliciesConstants;
                
				def maximumRequest = 5
                def cache = muleContext.getRegistry().get("cacheEmailRateLimiting")
                def key = "totalHits"
                def method = message.getInboundProperty("http.method")

                //we need to do this in order to avoid reporting a policy violation
                message.removeProperty(PoliciesConstants.POLICY_ID_FLOW_VARIABLE_NAME, PropertyScope.INVOCATION)
                message.removeProperty(PoliciesConstants.POLICY_NAME_FLOW_VARIABLE_NAME, PropertyScope.INVOCATION)
				
				//message.setInvocationProperty("cache", cache)
				message.setInvocationProperty("isAllowedToPass", true)
				message.setInvocationProperty("cachePolicyRequestCachingKey", key)
				
				def cacheEntry = cache.get(key);
				if (cacheEntry != null)
				{
					def totalHits = cacheEntry.getObjectValue()
					totalHits =  (totalHits as Integer) + 1
					
					if ((totalHits as Integer) > maximumRequest){
					   sleep(60000)
					   //message.setInvocationProperty("isAllowedToPass", false) 
					}	
				}
                return payload
            ]]></scripting:script>
    </scripting:component>
    <mule:message-filter onUnaccepted="notAllowedToPass">
      <mule:expression-filter expression="#[flowVars['isAllowedToPass']]"/>
    </mule:message-filter>
  </before>
  <after>
    <scripting:component>
        <scripting:script engine="Groovy"><![CDATA[
            import org.mule.api.config.MuleProperties
            import org.mule.api.store.ObjectAlreadyExistsException
            import java.util.Map
            import java.util.HashMap
            import net.sf.ehcache.Element
            import org.mule.transport.NullPayload

			def cache = muleContext.getRegistry().get("cacheEmailRateLimiting")
			def key = message.getInvocationProperty("cachePolicyRequestCachingKey")
			def cacheEntry = cache.get(key);
			if (cacheEntry != null)
			{
				def totalHits = cacheEntry.getObjectValue()
				totalHits =  (totalHits as Integer) + 1
				cache.put(new Element(key, totalHits))
            }else{
				cache.put(new Element(key, "1" as Integer))
			}
            return payload
        ]]></scripting:script>
    </scripting:component>
  </after>
  <!-- Pointcut defines where a policy implements. -->
      <pointcut>
		   <resource uriTemplateRegex="/test.*" />
		   <resource methodRegex="GET" />
      </pointcut>
</policy>

Article to test this go to Applying Custom Policies in On-prem Mule Runtime 3.9.1