An English merchant named William Bolt published a work called "Considerations of India Affairs", originally in 1772. Historian Romesh Chunder Dutt (in his book The Economic History of India - published in 1905) refers to this as a primary source because Bolt was writing from first-hand experience. This is what Dutt writes:

While the entire inland trade of Bengal was thus disorganised by the Company's servants and their agents in every important district, the methods by which they secured the manufactures to themselves were equally oppressive. These are fully described by William Bolts, an English merchant who saw things with his own eyes.

"... Weavers, also, upon their inability to perform such agreements as have been forced upon them by the Company's agents, universally known in Bengal by the name of Mutchulcahs, have had their goods seized and sold on the spot to make good the deficiency; and the winders of raw silk, called Nagaads, have been treated also with such injustice, that instances have been known of their cutting off their thumbs to prevent their being forced to wind silk."

Dutt is referring here specifically to the period between 1757 and 1765 - a period during which the Company had power over Bengal, and absolutely no responsibility. Essentially the Company's agents were able to go anywhere in Bengal, buy anything they wanted at whatever price they wanted at bayonet-point, and then sell it at whatever price they wanted. The issue was not what they were doing for the company - the company was steadily running into debt by this time. It was what they were doing in their personal capacities as private individuals.

What Bolt is saying is that this was so oppressive that weavers would cut off their thumbs to avoid being forced to weave, because this would presumably leave them free to do other work and hopefully feed their families. This was similar behavior to what they had been practicing in the Carnatic ever since the 1740's when they first helped put the Nawab of Arcot in power. The only reference I have states that they would make weavers "do whatever they wanted", but in Bengal it extended to all types of trade goods (basically they interpreted the post-Plassey treaty to mean they could trade all over Bengal without needing to pay any duties).

One thing to note is that plenty of Englishmen protested this behavior, including Warren Hastings (on the Council from 1761, and later Governor and then Governor-General) who even tried to negotiate a deal with Mir Kasim (the Nawab of Bengal) that would clearly define what the Company's agents could and could not do. Mir Kasim did his bit, but other than Henry Vansittart (Hasting's co-author on the deal), none in the Company's General Council supported this and instead protested loudly their right to "free trade". Well Mir Kasim responded with a genius move - he opened up free trade to all traders and merchants (at huge cost to the state), so the Company agents lost whatever advantage they had over the local traders. This led to war (and Mir Kasim's ultimate defeat at Buxar in October 1764). It is not clear (to me) when the abuses were finally stopped. The Company was eventually brought under the control of Parliament and in 1786 Lord Cornwallis made Company employees choose to either be traders or administrators - not both. This reduced their ability to abuse power and he was very particular in enforcing it. By then though the industrial revolution in England was making Indian cloth uncompetitive anyway. In 1813 for instance Lancashire textile merchants were quite excited about the breaking of the Company's monopoly that would let them sell in India.

In short Company agents did cause the thumb cutting incidents, but those are a very minor part of a huge disaster that befell Bengal under early Company rule. They are more a symptom of Bengal getting "deindustrialized" not the cause.