Maybe my way to avoid the same error  will be helpful for you.

please check following point with consideration of sample code

1.control the inputfile component to be shown

    To show them after a button click and to hide them before next page rendering

2. do not use rerender attribute on the second button.

   I am not sure about the reason. but my code work wery well

Page block :
        <!-- attachment erea   --> 
        <apex:pageBlock title="attachment" id="fileblock">
          <apex:pageBlockSection showHeader="true" title="File List" columns="4" id="Innfileblock">
                <apex:pageBlockTable value="{!erAttachInn}" var="file">
                    <apex:column >
                        <apex:commandbutton action="{!deleteAttachFile}" value="delete" reRender="Innfileblock">
                             <apex:param name="afparam1" value="{!file.id}" assignTo="{!attachIdTodel}"/>
                             <apex:param name="afparam2" value="erinn" assignTo="{!attchdomain}"/>
                        </apex:commandbutton>
                    </apex:column> 
                    <apex:column value="{!file.name}"/>
                    <apex:column value="{!file.description}"/>
                    <apex:column >
                         <apex:outputLink value="/servlet/servlet.FileDownload?file={!file.id}" id="theLink" target="_blank">⇒view this file</apex:outputLink>
                    </apex:column>                                                  
                </apex:pageBlockTable> 
     
           </apex:pageBlockSection> 

          <apex:pageBlockSection showHeader="true" title="new file erea " columns="4" id="Newfileblock">
               <apex:panelGrid id="newfilepanel" columns="1">
                 <apex:commandbutton action="{!addnewfile}" styleclass="button1" value="show new file component" reRender="fileblock" rendered="{!loadstep='step1'}">
                  </apex:commandbutton>                
                 <apex:commandbutton action="{!decidenewfile}" styleclass="button2" value="add this file to list"  rendered="{!loadstep='step2'}" >
                  </apex:commandbutton>
            </apex:panelGrid>           
           </apex:pageBlockSection> 
          <apex:pageBlockSection showHeader="false" columns="2" id="fileselect" rendered="{!loadstep='step2'}">
            <apex:pageBlockSectionItem >
                <apex:outputLabel value="domain" for="attachdomain"/>
                <apex:selectRadio value="{!newfile.attachdomain}" id="attachdomain">
                    <apex:selectOption itemValue="erInn" />
                    <apex:selectOption itemValue="erOut"/>
                    <apex:selectOption itemValue="ea" />
                </apex:selectRadio>
            </apex:pageBlockSectionItem>          
     
            <apex:pageBlockSectionItem >
              <apex:outputLabel value="file name" for="fileName"/>
              <apex:inputText value="{!newfile.attachment.name}" id="fileName"/>
            </apex:pageBlockSectionItem>
     
            <apex:pageBlockSectionItem >
              <apex:outputLabel value="file" for="file"/>
              <apex:inputFile value="{!newfile.attachment.body}" filename="{!newfile.attachment.name}" id="file"/>
            </apex:pageBlockSectionItem>
     
            <apex:pageBlockSectionItem >
              <apex:outputLabel value="description " for="description"/>
              <apex:inputTextarea value="{!newfile.attachment.description}" id="description"/>
            </apex:pageBlockSectionItem>
     
          </apex:pageBlockSection>
       
        </apex:pageBlock>

Part of controller
    // to show the inputfile component
    public void addnewfile() 
    {
        newfile=new AttachmentController();
        loadstep='step2';
    }


    // to add the new file to list
    public void decidenewfile() 
    {
        if(newfile.attachdomain=='erInn'){
            erAttachInn.add(newfile.attachment);
        }
        loadstep='step1';
        newfile=null;
    }