因为我不清楚你具体的语境,所以我就把以上你所提及到的这几句比较重要的话给你翻译一下,然后你自己加一下前后的基本问候语就行!
(你们公司）没有按照合同规定进行装运：Your company didn't follow the contract to ship.
经调查(我们发现它）确实存在问题：After the investigation,we found there were some problems of it indeed.
卖方表示歉意并允许提供5%的折扣：The seller is going to apologize and allow you a discount of 5%.
有什么需要的可以告诉我!