The Dow Jones Industrial Average climbed 2.47 points to 17789.67, while the wider S&P 500 index gained 2.37 to 2099.33.
The tech-focused Nasdaq edged up 4.2 points to 4952.25.
A larger than expected slowdown in car sales however sent shares of US carmakers tumbling.
Ford shares lost 2.8% after reporting a 5.9% fall in May sales.
Similarly General Motors fell 3.4% after the US carmaker reported sales for May were down 18% compared to the previous year.
Data showed global manufacturing slipped for another month, but US investors are waiting for employment data out Friday to get a better sense of whether the Federal Reserve will raise interest rates in June.
"There's an abundance of economic data this week that investors are confused on how to digest," said Jonathan Corpina, senior managing partner for Meridian Equity Partners.
Ecommerce firm Alibaba tumbled 6.5% after its largest investor announced a plan to sell its shares. Japan's SoftBank said it would sell $7.9bn worth of Alibaba shares to pay off some of its own debt.
Sportswear company Under Armour saw its shares fall 4%. The company warned investors on Wednesday that its results would be hurt by the bankruptcy of the sporting goods chain Sports Authority.
Shares in Michael Kors rose 6.6% to $44.85 after the handbag and accessories retailer reported a big rise in fourth-quarter revenues.
Revenue in the three months to 2 April rose 10.9% to $1.2bn, although this was helped by the opening of 142 new stores over the past year.
Same-store sales - seen as a better measure of underlying strength - rose by 0.3%, which Neil Saunders, of retail analysts Conlumino, described as "anaemic".
(Closed): Wall Street markets rose on Wednesday despite poor data from the manufacturing, housing and car industries.