Fix Error While Patching Security Patch SUPEE-6285

While trying to patch magento, which I have done a few times now with prior patches successfully, I encountered an issue with this latest patch.

Checking if patch can be applied/reverted successfully...
ERROR: Patch can't be applied/reverted successfully.

patching file app/Mage.php
patching file app/code/community/Phoenix/Moneybookers/controllers/MoneybookersController.php
patching file app/code/core/Mage/Adminhtml/Controller/Action.php
patching file app/code/core/Mage/Adminhtml/controllers/AjaxController.php
patching file app/code/core/Mage/Adminhtml/controllers/Catalog/Category/WidgetController.php
patching file app/code/core/Mage/Adminhtml/controllers/Catalog/Product/DatafeedsController.php
patching file app/code/core/Mage/Adminhtml/controllers/Catalog/Product/ReviewController.php
patching file app/code/core/Mage/Adminhtml/controllers/Catalog/Product/WidgetController.php
patching file app/code/core/Mage/Adminhtml/controllers/Cms/Block/WidgetController.php
patching file app/code/core/Mage/Adminhtml/controllers/Cms/Page/WidgetController.php
patching file app/code/core/Mage/Adminhtml/controllers/Cms/PageController.php
patching file app/code/core/Mage/Adminhtml/controllers/Cms/WysiwygController.php
patching file app/code/core/Mage/Adminhtml/controllers/Customer/System/Config/ValidatevatController.php
patching file app/code/core/Mage/Adminhtml/controllers/JsonController.php
patching file app/code/core/Mage/Adminhtml/controllers/NotificationController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/CustomerController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/ProductController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/ReviewController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/SalesController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/ShopcartController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/TagController.php
patching file app/code/core/Mage/Adminhtml/controllers/ReportController.php
patching file app/code/core/Mage/Adminhtml/controllers/Rss/CatalogController.php
patching file app/code/core/Mage/Adminhtml/controllers/Rss/OrderController.php
patching file app/code/core/Mage/Adminhtml/controllers/Sales/Billing/AgreementController.php
patching file app/code/core/Mage/Adminhtml/controllers/Sales/Order/View/GiftmessageController.php
patching file app/code/core/Mage/Adminhtml/controllers/Sales/Recurring/ProfileController.php
patching file app/code/core/Mage/Adminhtml/controllers/Sales/TransactionsController.php
patching file app/code/core/Mage/Adminhtml/controllers/System/Config/System/StorageController.php
patching file app/code/core/Mage/Adminhtml/controllers/TagController.php
patching file app/code/core/Mage/Adminhtml/controllers/Tax/RateController.php
patching file app/code/core/Mage/Adminhtml/controllers/TaxController.php
patching file app/code/core/Mage/Api2/controllers/Adminhtml/Api2/AttributeController.php
patching file app/code/core/Mage/Bundle/controllers/Adminhtml/Bundle/SelectionController.php
patching file app/code/core/Mage/Captcha/controllers/Adminhtml/RefreshController.php
patching file app/code/core/Mage/Centinel/controllers/Adminhtml/Centinel/IndexController.php
patching file app/code/core/Mage/Checkout/controllers/MultishippingController.php
patching file app/code/core/Mage/Connect/controllers/Adminhtml/Extension/LocalController.php
patching file app/code/core/Mage/ImportExport/Model/Abstract.php
Hunk #1 succeeded at 89 with fuzz 2 (offset -6 lines).
patching file app/code/core/Mage/Oauth/controllers/Adminhtml/Oauth/AuthorizeController.php
patching file app/code/core/Mage/Paygate/controllers/Adminhtml/Paygate/Authorizenet/PaymentController.php
patching file app/code/core/Mage/Paypal/controllers/Adminhtml/Paypal/ReportsController.php
patching file app/code/core/Mage/Rss/controllers/CatalogController.php
patching file app/code/core/Mage/Rss/controllers/OrderController.php
patching file app/code/core/Mage/Widget/Block/Adminhtml/Widget/Chooser.php
patching file app/code/core/Mage/Widget/controllers/Adminhtml/WidgetController.php
patching file app/design/frontend/base/default/template/checkout/cart.phtml
Hunk #1 succeeded at 99 (offset 1 line).
patching file app/design/frontend/base/default/template/checkout/cart/noItems.phtml
Hunk #1 FAILED at 31.
1 out of 1 hunk FAILED -- saving rejects to file app/design/frontend/base/default/template/checkout/cart/noItems.phtml.rej
patching file app/design/frontend/base/default/template/checkout/onepage/failure.phtml
patching file app/design/frontend/base/default/template/rss/order/details.phtml
patching file app/design/frontend/base/default/template/wishlist/email/rss.phtml
can't find file to patch at input line 894
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|diff --git app/design/frontend/default/modern/template/checkout/cart.phtml app/design/frontend/default/modern/template/checkout/cart.phtml
|index 43698c2..f4fe5ab 100644
|--- app/design/frontend/default/modern/template/checkout/cart.phtml
|+++ app/design/frontend/default/modern/template/checkout/cart.phtml
--------------------------
File to patch: 
Skip this patch? [y] 
Skipping patch.
1 out of 1 hunk ignored
patching file downloader/Maged/.htaccess
patching file downloader/Maged/Controller.php
patching file downloader/Maged/Model/Session.php
patching file downloader/lib/.htaccess
patching file downloader/template/connect/packages.phtml
patching file downloader/template/connect/packages_prepare.phtml
patching file downloader/template/login.phtml
patching file downloader/template/settings.phtml
patching file errors/processor.php

So my first move is to go look at the .rej files it creates which I assume declare what the disconnects are. However the file isn't there. Which led me to think possibly the folder doesn't have write access, but it does. So I am confused as to what could be going wrong, any ideas?

Magento Version: CE 1.9.0.1

Patch: PATCH_SUPEE-6285_CE_1.9.1.1_v1-2015-07-07-09-03-34.sh

Also; It is stated with the patch that you must first implement SUPEE-5994 to ensure SUPEE-6285 works properly, which I have already done.

EDIT: Turns out at some point, I deleted the /modern/ folder when it wasn't being used. Replacing that removed the cart.phtml issue, however the noItems.phtml issue still persists.