This issue you are facing with aggregate institutional ownership can be due to 3 reasons:
1. Special cases with high levels of institutional ownership and high short interest ratios around calendar quarter ends. 13F filings report only stock holdings and do not report short positions. See SEC 13F FAQ for more information: http://www.sec.gov/divisions/investment/13ffaq.htm.
2. Data error due to double counting that results from multiple filing of the same security holdings by institutions that share investment discretion over some parts of their assets under management. That's why you found similar cases in Yahoo. Note that while Thomson makes every effort to eliminate duplicate shareholdings in cases of shared investment discretion among multiple institutional managers who file 13f, there might be some cases with fractional institutional ownership > 1 (check Gompers Ishii and Metrick, QJE, 2001, "Institutional Investors and Equity Prices").
3. Incorrect shares outstanding in Thomson. We recommend that you use CRSP shares outstanding for this purpose. When summing over institutional holdings, you need to make sure first that all shares are adjusted for splits and special distributions. To do this, you need to use the fdate (Thomson file date) and CRSP cumulative adjustment factors. Also, we recommend that you use shares outstanding figures from CRSP data (make sure you adjust them as well). After you do this, then you will be able to sum all shareholding for each report date (rdate), and divide this figure by the total shares outstanding. In order to properly adjust for splits and special distributions, you need to merge Thomson data with CRSP cumulative adjusted factors (from monthly stock files) using the fdate in thomson (which is the file date) and date variable in CRSP. Please read the footnote in Thomson documentation for more information about fdate vs. rdate.