On Automation, an account's Today is its day so far, closed and open trades together. The Journal holds closed trades only, and works out the P&L of each. When the two differ for a day, fees and timing are the usual reasons.
Are fees taken off?
Where your broker reports a trade's fees, yes: the Journal's P&L is after them, and Net P&L on the Dashboard shows their total. Accounts on a Simulated connection are charged none.
A trade with no fees from its broker shows Not reported under Fees, and its P&L is the price move alone, before fees. Net P&L, the month and a day you open in Calendar, and each row of the tables in Reports say how many such trades they hold, such as 3 trades before fees. Your broker may already have taken those fees off its own figures, so on such a day the Journal can read higher than Automation. A P&L Card says Net profit & loss only when every trade on it had its fees reported.
When a trade's fees count
All of a trade's fees count on the day it closes, while your broker may charge part of them when the position opens. So a day can differ, for example:
while a position is still open: it is in Today on Automation, and not yet in the Journal;
after a position was held overnight: any fees charged when it opened are on the day before at your broker, and on the day it closed here.
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