Can a person be charged with two or more separate and distinct crimes arising from or based on the same act/incident?

Yes. 

A single act can give rise to charges of two or more distinct and separate crimes. This was the ruling in Lumauig vs. People, G.R. No. 166680, 7 July 2014, where the Supreme Court held that two or more charges may be brought against an accused based on the same incident, especially if there is a variance between the elements of the offenses charged.

In Lumauig, the Accused was charged with the crimes of Failure to Render an Account under Article 218 of the Revised Penal Code (RPC) and violation of Section 3(e) of Republic Act No. 3019 (RA 3019), arising from his failure to liquidate a cash advance in his favor within the time required therefor.

After trial, the trial court acquitted the accused of the anti-graft charge, but convicted him under Article 218 of the RPC since he admittedly failed to liquidate the cash advance released to him within the pertinent period.

The accused contested his conviction and claimed that his acquittal under Section 3(e) of RA 3019 should bar his conviction under Article 218 of the RPC considering that the cases against him involve the same cash advance. In other words, he argued that his exoneration in the anti-graft case should exculpate him from further liability under Article 218 of the RPC.

The Supreme Court rejected the said arguments and held that it was not impossible for the accused to be charged with 2 separate crimes in this case, since the elements under the said offenses differ, even if both cases may hinge on the same set of evidence, thus -

"It is undisputed that the two charges stemmed from the same incident.' However, [we have] consistently held that the same act may give rise to two or more separate and distinct charges." Further, because there is a variance between the elements of the two offenses charged, petitioner cannot safely assume that his innocence in one case will extend to the other case even if both cases hinge on the same set of evidence. 

To hold a person criminally liable under Section 3 (e) of RA 3019, the following elements must be present: 

(1) That the accused is a public officer or a private person charged in conspiracy with the former; 

(2) That said public officer commits the prohibited acts during the performance of his or her official duties or in relation to his or her public positions; 

(3) That he or she causes undue injury to any party, whether the government or a private party; 

(4) That such injury is caused by giving unwarranted benefits, advantage or preference to such parties; and 

(5) That the public officer has acted with manifest partiality, evident bad faith or gross inexcusable negligence. 

On the other hand, the elements of the felony punishable under Article 218 of the Revised Penal Code are: 

(1) That the offender is a public officer whether in the service or separated therefrom; 

(2) That he must be an accountable officer for public funds or property; 

(3) That he is required by law or regulation to render accounts to the COA or to a provincial auditor; and, 

(4) That he fails to do so for a period of two months after such account should be rendered. 

The glaring differences between the elements of these two offenses necessarily imply that the requisite evidence to establish the guilt or innocence of the accused would certainly differ in each case. Hence, petitioner's acquittal in the anti-graft case provides no refuge for him in the present case given the differences between the elements of the two offenses." (Emphasis and underscoring supplied)

Given the foregoing, the high court upheld the conviction of the accused under Article 218 of the RPC, notwithstanding his acquittal under Section 3(e) of RA 3019.

The test, therefore, is not whether or not the there is only a single act, but whether the crimes against which the accused is charged have the same or similar elements, such that one crime is absorbed or absorbs the other.