In April, the firm sold 4.1 million of the shares it had in Canadian Pacific, which at the time reduced its overall stake by 30 percent.

Pershing Square has suffered outsize losses on several stocks in its portfolio — most notably Valeant Pharmaceuticals. The troubled drug company’s shares have fallen 78 percent this year as it has come under pressure for its pricing strategies and for some of its sales distribution practices. Mr. Ackman is now a member of Valeant’s board and has told investors that he intends to take a hands-on approach to overseeing the company’s turnaround.

The hedge fund’s big bearish bet on Herbalife, the nutritional food supplement company, worked against it once again this year. Shares of Herbalife are up 24 percent this year even after the company paid $200 million to the Federal Trade Commission to settle an investigation into its business practices.

The settlement with the F.T.C., however, was something of a moral victory for Mr. Ackman, who has waged a high-octane campaign against Herbalife, claiming it is an unlawful pyramid scheme that takes advantage of its customers — many of whom are either poor or of modest means. The F.T.C. stopped short of calling Herbalife a pyramid scheme and ordering it to shut down. But the regulatory agency did charge the company with “deceiving hundreds of thousands of hopeful people,” and directed it to make substantial changes to its sales practices and hire an outside monitor to oversee its activities.

Mr. Ackman has said his firm is maintaining its “short” bet, which will prove profitable if Herbalife’s stock price collapses. Mr. Ackman has said Herbalife’s revenue and profit will tumble if it changes its business practices as the F.T.C. has ordered.

Canadian Pacific has been one of Pershing Square’s better-performing investments. The firm began buying shares and establishing a big stake in the company in 2011, when the stock was selling for just under $50. Pershing Square would go on to win a proxy contest to install new board members and ultimately E. Hunter Harrison as chief executive.