Magento 2 Apache Rewrites Not Working Locally – Troubleshooting Guide

Try to reindex your URL rewrites. You are able to do it using shell in Magento EE 13+

cd [magento_root]/shell
php indexer.php --reindex catalog_url

If it didn't help:
Try to open some of the products in admin panel for editing and try to save it. Then, try to check the product's URL in the rewrite tables once again. Maybe the reason is the products were imported incorrectly somehow. If that way is solving your issue : You can make a script - just get products collection and save each product without making changes

$products = Mage::getModel('catalog/product')->getCollection();
foreach ($products as $_product) {
    $_product->save();
}

Also, you can add a try..catch structure in case if you have a problem with the product's saving.

Your .htaccess file is not loaded or does not contain the rewrite section and/or your vhost file from apache does not contain the correct section.

For conf file

 <Directory /home/path/to/html>
       AllowOverride All
       Order allow,deny
       Allow from all
</Directory>

For .htaccess

<IfModule mod_rewrite.c>

############################################
## enable rewrites

    Options +FollowSymLinks
    RewriteEngine on

############################################
## you can put here your magento root folder
## path relative to web root

    #RewriteBase /magento/

############################################
## uncomment next line to enable light API calls processing

#    RewriteRule ^api/([a-z][0-9a-z_]+)/?$ api.php?type=$1 [QSA,L]

############################################
## rewrite API2 calls to api.php (by now it is REST only)

    RewriteRule ^api/rest api.php?type=rest [QSA,L]

############################################
## workaround for HTTP authorization
## in CGI environment

    RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]

############################################
## TRACE and TRACK HTTP methods disabled to prevent XSS attacks

    RewriteCond %{REQUEST_METHOD} ^TRAC[EK]
    RewriteRule .* - [L,R=405]

############################################
## redirect for mobile user agents

    #RewriteCond %{REQUEST_URI} !^/mobiledirectoryhere/.*$
    #RewriteCond %{HTTP_USER_AGENT} "android|blackberry|ipad|iphone|ipod|iemobile|opera mobile|palmos|webos|googlebot-mobile" [NC]
    #RewriteRule ^(.*)$ /mobiledirectoryhere/ [L,R=302]

############################################
## always send 404 on missing files in these folders

    RewriteCond %{REQUEST_URI} !^/(media|skin|js)/

############################################
## never rewrite for existing files, directories and links

    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteCond %{REQUEST_FILENAME} !-l

############################################
## rewrite everything else to index.php

    RewriteRule .* index.php [L]

</IfModule>