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It's not pointing in the wrong direction, it's pointing in the direction the current is flowing, you can add an absolute function to the plot trace if you want. Post the schematic you're talking about, a screenshot with the trace would be handy for people that don't use LTSpice as well so we know what you're talking about.
What do you mean by "current probe"? Are you plotting current through a two-pin component, like a resistor? If so, then use the MOVE function to swap ends of the resistor in-place, and then resim. What was formerly a negative current will become a positive current, and vice-versa. Devices with multiple pins are defined with positive current flowing into the component. Also remember that positive current is defined as the direction that positive charge carriers flow, i.e. Conventional Current, NOT Electron current.
Stare at the attached LTSpice sim. All of the currents are consistent with what I said above. The only two currents that could be "reversed" are I(R1), and I(R2), and only because the resistor pins can actually be swapped in the schematic by physically mirroring the resistors.
LTSpice is capable of several types of analysis, only three of which are described below:
.DC=set all voltage/current sources to their initial or bias state, and solve for all node voltages and device current, and print them in tabular form.
This is also used to plot parametric sweeps, such as Vout vs Vin or Vout vs changing a resistor in steps.
.TRAN=plot node voltages and device currents vs time, after beginning with essentially a .DC solution first.
.AC=Plot Magnitude and Phase of voltages and currents as frequency is swept over octaves or decades. A .DC solution is done first to establish the operating points of all devices.
Note that I used .OP as the method of analysis in the circuit I posted.
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