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There are a number of challenges.
I would like pile on with the recommendations for using activeshare.info. However, active share data is only available for mutual funds, so the use cases are limited.
As your question title implies, "detecting" a managers active bets is a function of differentiating them from passive bets.
From Investopedia entry on 13-F "Alpha Cloning":
Portfolio managers can't pick stocks - this is a common saying in popular press and between proponents of index investments. But research shows it is not such an evident truth. Mutual/hedge fund managers in reality can pick stocks but are often too diversified and their "best picks" therefore cannot deliver such a spectacular performance as fund's performance is dragged down by rest of the portfolio. The 13F Fillings Following system is based on assumption that stocks in which mutual fund managers (and hedge fund managers) are mostly concentrated (their best ideas) are stocks which will outperform the broad equity index. SEC 13F fillings could be used to track top holdings positions in mutual funds.
When an appropriate benchmark is ambiguous (as is often the case for the general case of active management), treating every fund as its own benchmark overcomes the biases you mention in (1) and (2). This benchmark holds every stock in the manager's portfolio and weights each holding "passively". Passive weighting in this context usually means public float adjusted, since this requires also no active management and is what is reflect in most major indices. "Passive" can also be more broadly interpreted to mean any weighting schema which does not involve active bet sizing (e.g., equal weighting).
Treating each portfolio as it own benchmark gets around the issue of identifying active weighting. This method is most robust for funds with diversified holdings ($\ge 30 ???$) However, it is limited due to the fact that skill also involves active selection.
To detect fund manager's active stock picks from his portfolio holdings you need the managers' benchmark index. Check the fund fact sheet for this. Fund Rating Agencies often use a broad well-known index, but that index often does not fit to the origin fund investment approach. An American US Value oriented fund can consequently outperform his own index, but simultaneously underperform the broad main index. Therefore, the best way is to ask the fund company for an attribution analysis.
