Wholesale All In One app is partially compatible with the subscription application such as: 
Bold Subscription  and Recharge.

Rule of thumb

Wholesale All In One  app applies wholesale pricing to an order only when it processes with Shopify Default checkout and  it doesn't work when an order processes with a different checkout. 

Case#1 -  When does app not work?

Wholesale All In One app doesn't work when an order process with a different checkout rather than default Shopify checkout. 
For Example, When cart contains a product with 'subscription' option as selected then our wholesale app doesn't work, because in this case order will process with a different checkout.

Chase #2: When does app work? 

Wholesale app works with all other cases when order process with Default Shopify checkout such as: 
- Regular products that don't have subscription options. 
- When 'One time purchase' option is selected for subscription products.

Available Solution

Normally, we hide the subscription options for the wholesale customers. However, regular customers can still place the orders with subscription items. In order to hide the subscription option for wholesale customers, please write an email, Contact US