Dear Yumit,
Sorry to hear you are running into this issue. Having duplicate post metas is indeed a bad thing and should never happen. Codewise, we are using WooCommerce's WC_Order::update_meta_data, which should replace an existing post meta. We are not manipulating the database directly, where such duplicates might be expected.
Do you see those duplicate post metas with each order, or just with some orders?
I have tried reproducing this issue here at our local installations, but I couldn't. Here, each order (with the same ordernumber settings as shown in your screenshot) always gets just one post meta with key _oton_number_ordernumber...
Which versions of (a) our plugin, (b) WooCommerce, (c) WordPress and (d) PHP do you use? Do you have any other plugins installed that might internally use sub-orders or the like? It's probably easiest if you can create the WooCommerce system report (in the backend, go to "WooCommerce -> Status", button "Get system report", then "Copy for support" and paste everything into an email to office@open-tools.net
That report contains detailed information about your installation, but should not contain any sensitive information. It might help us figure out what causes those duplicate post metas.
Best regards,
Reinhold