In fact, it has already happened in the past. Huobi and OKCoin have both been caught using users' deposits to invest in various high risk vehicles, meaning that they were no longer holding all the coins required to recover all their deposits, and were therefore fractional reserve: https://cointelegraph.com/news/two-chinese-exchanges-help-themselves-to-user-funds. I would bet every bitcoin I own that this practice is still ongoing on a number of exchanges. We also know other coins such as Tether are not backed up 1-to-1 as was previously claimed and are therefore fractional reserve.

As long as we have users trusting third party exchanges or web wallets with their coins, then we will always have the potential for a fractional reserve system to the risk of those users in question. The only way to avoid being subjected to fractional reserve is to hold your own coins. The only way to completely stop fractional reserve systems altogether is if everybody held their own coins.