Stock levels not deducting

Please see below the message i got form my client ?

what could be the cause of this ? where do i start

WooCommerce system status below ,, removes my website name to website.xxxxx

[12:02 PM, 1/29/2017] Joe: So the packing slip has 101 line items, the order has 101 line items but if you view the order and look at the notes where items deducted shows – there are only 58.
[12:03 PM, 1/29/2017]?Joe:?I am have to do 2 previous orders over – I have to look at the item number that was deducted mark which card it is then select the others and decrease stock for them.
[12:04 PM, 1/29/2017]?Joe:?Another order I have to do this twice as he put in 2 orders and both had this issue so have to increase stock deducted on the one then cancel that one then look which cards match the item numbers then decrease the other stock on the order that is left…

### WordPress Environment ###

Home URL: https://website.xxxxxxx
Site URL: https://website.xxxxxxx
WC Version: 2.6.13
Log Directory Writable: ?
WP Version: 4.5.6
WP Multisite: –
WP Memory Limit: 256 MB
WP Debug Mode: –
WP Cron: ?
Language: en_US

### Server Environment ###

Server Info: Apache mod_fcgid/2.3.9
PHP Version: 5.6.21
PHP Post Max Size: 50 MB
PHP Time Limit: 60
PHP Max Input Vars: 1000
cURL Version: 7.38.0
OpenSSL/1.0.1e

SUHOSIN Installed: –
MySQL Version: 5.6.33
Max Upload Size: 10 MB
Default Timezone is UTC: ?
fsockopen/cURL: ?
SoapClient: ?
DOMDocument: ?
GZip: ?
Multibyte String: ?
Remote Post: ?
Remote Get: ?

### Database ###

WC Database Version: 2.6.13
: 
woocommerce_sessions: ?
woocommerce_api_keys: ?
woocommerce_attribute_taxonomies: ?
woocommerce_downloadable_product_permissions: ?
woocommerce_order_items: ?
woocommerce_order_itemmeta: ?
woocommerce_tax_rates: ?
woocommerce_tax_rate_locations: ?
woocommerce_shipping_zones: ?
woocommerce_shipping_zone_locations: ?
woocommerce_shipping_zone_methods: ?
woocommerce_payment_tokens: ?
woocommerce_payment_tokenmeta: ?

### Active Plugins (28) ###

Activity Log: by Yakir Sitbon
Maor Chasen
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### Settings ###

Force SSL: –
Currency: ZAR (R)
Currency Position: left
Thousand Separator: ,
Decimal Separator: .
Number of Decimals: 2

### API ###

API Enabled: ?

### WC Pages ###

Shop Base: #1595 - /shop/
Cart: #1596 - /cart/
Checkout: #1597 - /checkout/
My Account: #887 - /my-account/

### Taxonomies ###

Product Types: external (external)
grouped (grouped)
simple (simple)
variable (variable)

### Theme ###

Name: CarZilla
Version: 2.1
Author URL: https://newwpthemes.com
Child Theme: ? – If you're modifying WooCommerce on a parent theme you didn't build personally
then we recommend using a child theme. See: How to create a child theme

WooCommerce Support: ?

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Overrides: –