My internet fees should count as business expense and be deducted from gross
Since I also use internet for entertainment etc, how can I prove myself when I say 50% of the internet fee should be deducted?
You can measure how much content you've downloaded or uploaded for your business and how much was not and prorate the costs accordingly. Alternatively you can measure how much time you spent using the internet for your business out of the total subscription period and prorate accordingly.
but I can also easily use UpWork for personal purposes. Again, how to prove and differentiate?
I'm guessing you get itemized invoices from these freelancers?
Maybe I overestimated my business expenses or did a wrong calculation
If you're "estimating" your business expenses then you're doing something wrong.
How will the IRS know/prove something is wrong and what are my penalties?
They'll audit you, and depending on what they find the penalties may be from 20% (accuracy related penalty under Sec. 6662) up to 75% of the income you've concealed (Sec. 6663 - fraud). For fraud you may also face criminal prosecution (under Sec. 7201, 7206, 7207, etc).
The audits may be random (you just got unlucky and selected for examination), or triggered by various "red flags" on your return, or due to information the IRS got from somewhere else (someone else's audit, tips, banks flagging suspicious transactions, other law enforcement referrals, etc).
How will the IRS know/prove something is wrong
They don't have to prove anything. You're the one who's required to prove the correctness of your return.