Occasionally, the Charles Schwab trade history data may be out of order for a specific date. This usually occurs when one has challenged a fill or has had another manual edit from customer service. Since the Charles Schwab transaction history does not include time of day for the trades, there is no automated way for any software program to determine the proper order of trades. And since TradeLog matches trades in a first-in first-out methodology, it is inevitable that trades may be mismatched when this happens. This is especially noted for very active intraday traders. In addition, the trade history data usually does not report when a buy is a "buy to cover" a short sale so this can make matching difficult also.
Charles Schwab does use timestamps for the purpose of their reporting cost basis to the IRS on 1099-B. You can view the order of transactions on their UGL and/or RGL tabs on schwab.com and compare that to TradeLog to reconcile any discrepancies.
To fix this, first run the Fix Trades Out of Order function if you receive negative share errors.
If trades are not properly matching the run the Edit, Force Match Trades function.