Common

In some marketplaces, some sellers prefer that the buyer purchase from them directly to save on marketplace fees.  If you do not buy directly, some sellers may start sending defective items. Though some money may be saved, it can be a disadvantage for both the seller and buyer.

Seller
Has to deal with a buyer who may file a chargeback after receiving the item.
No records are maintained
Bank details are revealed which can be misused.

Buyer
The seller may not ship the item after payment
The seller may send a defective or non working item
Bank details are revealed which can be misused.

An E-commerce website may spend a lot of time optimizing it and making it more user friendly, but for sales ,  there are certain factors the ecommerce website has little control of
In the Indian context the 2 major factors are:
1. Malware/ software installed on the customers PC
2. ISP connection

There are certain e-commerce and mutual funds websites on which a user cannot complete transactions with older computers (with Windows XP). These websites usually use Windows hosting and when you try to make a payment, there is a time out error. This problem does not exist on  a newer computer with Windows 7 installed on it . One option is to buy a new computer every few months or reformat your computer. Most internet users do not have multiple computers to try out different options, and will abandon the online transaction.

Sometimes, the ISP used can also make a difference. A transaction using one ISP connection may be flagged, while a similar transaction using a second ISP connection may not.

For online payments, the options available are:

• NEFT transfers
• bank account to account transfers
•  payment processors

For both NEFT transfers and bank a/c to a/c transfer you have to reveal your bank details to the party who is paying you. This can be risky if you are dealing with a stranger you may misuse your financial information. The individual may not transfer the funds electronically but deposit cash in your account and banks sometimes charge Rs 100 for cash deposits. 

If you a payment processor, you can be paid using debit card/ credit or bank  transfer. This is the main reason why payment processors are preferred worldwide  to direct person to person payments.

Though many people prefer to buy branded goods online, the margins for these products are fairly low and there is a lot of competition.  On the other hand, if you purchase directly from a  manufacturer, the margins are higher. However, most manufacturers will have a minimum order size, which is fairly large for some online retailers.