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Certainly can imagine this happens. Currently I'm scraping 4 banks and 4 shops on a daily basis, and the only issue was when scraping for the first time from new IP address. They asked a security question or displayed a captcha. I resolved this by logging in first time from the browser through SSH tunnel over that IP. All subsequent scraping went well since then.

Opposing personal experience - I've been scraping my bank data (scotia) for about a year now, haven't had any serious problems (there seems to be some kind of signin counter that thresholds and then forces secret questions to be reset, but that's it).

A concerted community effort could develop counter-heuristics.