This can occur if you have a lot of documents and customers that the system has to check against.
For each customer you have, the system has to check each document ID to see if that customer has access to the document or not. So if for example you have 2000 customers and 10000 documents there will be 20000000 queries on the database (2000 x 10000). For each individual customer lookup there is therefore 10,000 queries. If you have publications as well, then checks also need to be made against each user for each publication too.
To solve this:
You can export a list of your customers without document IDs (documents that they have been granted access to) by unchecking the box “Include Document Access”. You will then be able to successfully export your customer list.
You can also export a list of your customers without publication IDs by unchecking the box “Include Publication Access”. You may want to do this if you have a large number of publications.