Weve been having these issuues lately since I started activating mikrotik webproxy. First, for some websites, It will give you "gateway time out" with all those writings from webproxy, refreshing the page will allow you to go to the website, however they find it inconvenient,another thing is that some emails that were sent through outlook are not being delivered to recipients outside. If this wont stop, we might have issues implementing mikrotik to some other companies. Please give me some advise on what to do. Thanks.

another thing is that some emails that were sent through outlook are not being delivered to recipients outside.

I don't think outlook uses proxy, It connects directy to mail transfer agent (mail server), using ports 25|110|143|993 to send and receive mails (depending on security ssl, tls, etc...)
unless you have configured transparent proxy and have redirected one of these ports, outlook is not affected by webproxy (I can't imagine another situation).

What does it means recipients outside?, do you have a mail server on your LAN ?
I've had an internal mail server for years in my company, so mails delivered inside the domain didn't went out the LAN.
This saved a lot of traffic and security problems, but had the problem of mailing to N recipients outside should send N mails separately (10 photos of holidays without srhinking to 50 "friends" = 500 mb * 1,3 due to base64 encoding= 650mb of "spam")

First, for some websites, It will give you "gateway time out"

Do you have more than one adsl ?
Maybe routes an marking rules are not correct?

I bet you'll have to describe a bit your configuration to guess what is happening (rules and rutes)