I have to agree with Tank here. Lois, having her privacy invaded, would have gone ballistic against Lex. If she were in her right mind (big "if" in this arc), she wouldn't have cared how she found out and would have told off Luthor before handing him his walking papers for not trusting her. If she's upset at Clark being there to check up on her, what does she think video cameras and phone taps are for? Yet she's ready to crucify Clark and let Luthor off the hook for doing exactly the same thing.
As for Clark, she's appropriately upset at Clark and very confused, but she seems to have completely written him off as a romantic partner and is now concentrating exclusively on Luthor as her "maybe soon to be fiance," which sounds very much like she's leaning towards saying yes, odd given the bugging of her office. She thinks of Clark only in the terms of whether she even wants to be his friend or not, not whether she wants to be involved with him, be his friend, or neither.
If Clark is actually there to investigate Luthor, she would be unjustified in being angry at him, not that that would stop her. What business is it of hers what he does? If he wants to waste his time investigating such an honest man, that should teach him. Clark should ask her to help him investigate, just to get a reaction out of her. 'Fess up about it. At this point in time, Lois rolls over for just about any misdeed of Luthor's, while at the same time is upset at everything Clark does. If she turns him in, he's justified in writing her off. Of course, she'll fry him for checking up on her, even if it's to find out whether she'll spill the beans on his secret identity.
I like the fact that Lois is automatically covering for Clark now when he has to venture off to be Superman.
Also, Missy introduced Clark as the newest anchor man, but Lois just sent him out on an assignment. I wonder what the producer is going to say when he/she finds out that Lois sent an on air personality out into the field?
As for Clark being told by Lois to investigate a story, it's not necessarily in the field. Being an executive, isn't it her job to tell these people what to do?
Nice setup for the next part, where I'll guess the next writer will have the meeting between L&C.